Starting phenix.real_space_refine on Mon Mar 25 03:26:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/03_2024/6z3a_11055_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/03_2024/6z3a_11055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/03_2024/6z3a_11055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/03_2024/6z3a_11055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/03_2024/6z3a_11055_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/03_2024/6z3a_11055_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.323 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 194 5.16 5 C 29704 2.51 5 N 7680 2.21 5 O 8556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 60": "NH1" <-> "NH2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "F ARG 464": "NH1" <-> "NH2" Residue "F PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 520": "NH1" <-> "NH2" Residue "F ARG 549": "NH1" <-> "NH2" Residue "F ARG 582": "NH1" <-> "NH2" Residue "F ARG 585": "NH1" <-> "NH2" Residue "F ARG 794": "NH1" <-> "NH2" Residue "F TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 985": "NH1" <-> "NH2" Residue "F TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1260": "NH1" <-> "NH2" Residue "F ARG 1393": "NH1" <-> "NH2" Residue "F ARG 1403": "NH1" <-> "NH2" Residue "F ARG 1412": "NH1" <-> "NH2" Residue "F ARG 1422": "NH1" <-> "NH2" Residue "F ARG 1456": "NH1" <-> "NH2" Residue "F PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1498": "NH1" <-> "NH2" Residue "F ARG 1760": "NH1" <-> "NH2" Residue "F ARG 1809": "NH1" <-> "NH2" Residue "F TYR 1832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1845": "NH1" <-> "NH2" Residue "F PHE 1854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1870": "NH1" <-> "NH2" Residue "F ARG 1949": "NH1" <-> "NH2" Residue "F ARG 1961": "NH1" <-> "NH2" Residue "F ARG 1983": "NH1" <-> "NH2" Residue "F ARG 2048": "NH1" <-> "NH2" Residue "F ARG 2123": "NH1" <-> "NH2" Residue "F ARG 2161": "NH1" <-> "NH2" Residue "F ARG 2263": "NH1" <-> "NH2" Residue "F ARG 2293": "NH1" <-> "NH2" Residue "F ARG 2310": "NH1" <-> "NH2" Residue "F ARG 2328": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 664": "NH1" <-> "NH2" Residue "C ARG 704": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 664": "NH1" <-> "NH2" Residue "D ARG 704": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 352": "NH1" <-> "NH2" Residue "E ARG 353": "NH1" <-> "NH2" Residue "E PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "E ARG 464": "NH1" <-> "NH2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E ARG 520": "NH1" <-> "NH2" Residue "E ARG 549": "NH1" <-> "NH2" Residue "E ARG 582": "NH1" <-> "NH2" Residue "E ARG 585": "NH1" <-> "NH2" Residue "E ARG 794": "NH1" <-> "NH2" Residue "E TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 985": "NH1" <-> "NH2" Residue "E TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1260": "NH1" <-> "NH2" Residue "E ARG 1393": "NH1" <-> "NH2" Residue "E ARG 1403": "NH1" <-> "NH2" Residue "E ARG 1412": "NH1" <-> "NH2" Residue "E ARG 1422": "NH1" <-> "NH2" Residue "E ARG 1456": "NH1" <-> "NH2" Residue "E PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E ARG 1760": "NH1" <-> "NH2" Residue "E ARG 1809": "NH1" <-> "NH2" Residue "E TYR 1832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1845": "NH1" <-> "NH2" Residue "E PHE 1854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1870": "NH1" <-> "NH2" Residue "E ARG 1949": "NH1" <-> "NH2" Residue "E ARG 1961": "NH1" <-> "NH2" Residue "E ARG 1983": "NH1" <-> "NH2" Residue "E ARG 2048": "NH1" <-> "NH2" Residue "E ARG 2123": "NH1" <-> "NH2" Residue "E ARG 2161": "NH1" <-> "NH2" Residue "E ARG 2263": "NH1" <-> "NH2" Residue "E ARG 2293": "NH1" <-> "NH2" Residue "E ARG 2310": "NH1" <-> "NH2" Residue "E ARG 2328": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46142 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 18496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2311, 18496 Classifications: {'peptide': 2311} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2242} Chain breaks: 9 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 155 Chain: "C" Number of atoms: 4541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4530 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 554, 4530 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4606 Chain: "D" Number of atoms: 4545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4534 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 554, 4534 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 4610 Chain: "E" Number of atoms: 18496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2311, 18496 Classifications: {'peptide': 2311} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2242} Chain breaks: 9 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 155 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3770 SG CYS F 490 36.075 153.497 110.956 1.00207.44 S ATOM 3794 SG CYS F 493 35.634 157.327 111.749 1.00173.90 S ATOM 31201 SG CYS E 467 100.788 69.602 110.218 1.00214.30 S ATOM 31352 SG CYS E 490 97.402 68.950 110.769 1.00206.97 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG C 228 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 228 " occ=0.50 residue: pdb=" N AARG D 228 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 228 " occ=0.50 Time building chain proxies: 27.41, per 1000 atoms: 0.59 Number of scatterers: 46142 At special positions: 0 Unit cell: (134.62, 223.66, 177.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 194 16.00 P 6 15.00 O 8556 8.00 N 7680 7.00 C 29704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.28 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E2402 " pdb="ZN ZN E2402 " - pdb=" NE2 HIS E 553 " pdb="ZN ZN E2402 " - pdb=" SG CYS E 490 " pdb="ZN ZN E2402 " - pdb=" SG CYS E 467 " pdb=" ZN F2402 " pdb="ZN ZN F2402 " - pdb=" NE2 HIS F 553 " pdb="ZN ZN F2402 " - pdb=" SG CYS F 490 " pdb="ZN ZN F2402 " - pdb=" SG CYS F 493 " 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 279 helices and 4 sheets defined 59.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.29 Creating SS restraints... Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.661A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 removed outlier: 3.940A pdb=" N ASN F 49 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN F 54 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 83 removed outlier: 3.749A pdb=" N LEU F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 99 through 112 removed outlier: 3.711A pdb=" N ASP F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 132 removed outlier: 3.662A pdb=" N MET F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 139 through 160 removed outlier: 4.255A pdb=" N LYS F 143 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE F 144 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR F 147 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA F 148 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE F 150 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET F 154 " --> pdb=" O GLU F 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 158 " --> pdb=" O ASN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 172 through 188 removed outlier: 3.781A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 228 removed outlier: 3.528A pdb=" N ASN F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 252 removed outlier: 3.559A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.609A pdb=" N ASN F 284 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.881A pdb=" N LYS F 313 " --> pdb=" O ASP F 310 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 318 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 354 Processing helix chain 'F' and resid 391 through 405 removed outlier: 4.480A pdb=" N PHE F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.669A pdb=" N LEU F 436 " --> pdb=" O PHE F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 471 removed outlier: 3.597A pdb=" N CYS F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 503 No H-bonds generated for 'chain 'F' and resid 501 through 503' Processing helix chain 'F' and resid 512 through 515 No H-bonds generated for 'chain 'F' and resid 512 through 515' Processing helix chain 'F' and resid 517 through 528 removed outlier: 3.840A pdb=" N LEU F 527 " --> pdb=" O HIS F 523 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 552 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 582 through 588 Processing helix chain 'F' and resid 592 through 595 No H-bonds generated for 'chain 'F' and resid 592 through 595' Processing helix chain 'F' and resid 606 through 617 removed outlier: 4.139A pdb=" N SER F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 637 removed outlier: 3.576A pdb=" N LYS F 624 " --> pdb=" O PRO F 621 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU F 625 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN F 626 " --> pdb=" O VAL F 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 629 " --> pdb=" O ASN F 626 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN F 633 " --> pdb=" O ALA F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 654 removed outlier: 3.838A pdb=" N ILE F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 675 Processing helix chain 'F' and resid 680 through 695 Proline residue: F 686 - end of helix Proline residue: F 689 - end of helix removed outlier: 3.954A pdb=" N ARG F 693 " --> pdb=" O PRO F 689 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 694 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU F 695 " --> pdb=" O LEU F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 703 through 713 Processing helix chain 'F' and resid 717 through 727 removed outlier: 4.494A pdb=" N ILE F 723 " --> pdb=" O THR F 719 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG F 726 " --> pdb=" O ASP F 722 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR F 727 " --> pdb=" O ILE F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 733 removed outlier: 4.177A pdb=" N ILE F 733 " --> pdb=" O PRO F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 748 Processing helix chain 'F' and resid 756 through 766 Processing helix chain 'F' and resid 769 through 777 Processing helix chain 'F' and resid 784 through 792 Processing helix chain 'F' and resid 806 through 808 No H-bonds generated for 'chain 'F' and resid 806 through 808' Processing helix chain 'F' and resid 810 through 816 Processing helix chain 'F' and resid 828 through 842 Processing helix chain 'F' and resid 845 through 847 No H-bonds generated for 'chain 'F' and resid 845 through 847' Processing helix chain 'F' and resid 861 through 863 No H-bonds generated for 'chain 'F' and resid 861 through 863' Processing helix chain 'F' and resid 869 through 891 removed outlier: 4.444A pdb=" N LEU F 881 " --> pdb=" O GLN F 877 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY F 882 " --> pdb=" O ASP F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 915 Processing helix chain 'F' and resid 919 through 924 Processing helix chain 'F' and resid 928 through 938 Processing helix chain 'F' and resid 943 through 955 Processing helix chain 'F' and resid 963 through 965 No H-bonds generated for 'chain 'F' and resid 963 through 965' Processing helix chain 'F' and resid 967 through 979 removed outlier: 6.886A pdb=" N SER F 978 " --> pdb=" O LEU F 974 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU F 979 " --> pdb=" O GLN F 975 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 998 Processing helix chain 'F' and resid 1000 through 1003 No H-bonds generated for 'chain 'F' and resid 1000 through 1003' Processing helix chain 'F' and resid 1008 through 1016 Processing helix chain 'F' and resid 1022 through 1025 No H-bonds generated for 'chain 'F' and resid 1022 through 1025' Processing helix chain 'F' and resid 1028 through 1038 removed outlier: 4.130A pdb=" N ARG F1031 " --> pdb=" O GLN F1028 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F1037 " --> pdb=" O ASN F1034 " (cutoff:3.500A) Processing helix chain 'F' and resid 1042 through 1051 removed outlier: 3.953A pdb=" N LYS F1051 " --> pdb=" O ALA F1047 " (cutoff:3.500A) Processing helix chain 'F' and resid 1055 through 1075 Processing helix chain 'F' and resid 1091 through 1104 Processing helix chain 'F' and resid 1110 through 1123 Processing helix chain 'F' and resid 1149 through 1164 Processing helix chain 'F' and resid 1174 through 1190 Processing helix chain 'F' and resid 1207 through 1214 Processing helix chain 'F' and resid 1218 through 1227 removed outlier: 3.699A pdb=" N TYR F1225 " --> pdb=" O LYS F1221 " (cutoff:3.500A) Proline residue: F1226 - end of helix Processing helix chain 'F' and resid 1246 through 1251 Processing helix chain 'F' and resid 1257 through 1267 Processing helix chain 'F' and resid 1275 through 1281 removed outlier: 3.760A pdb=" N PHE F1279 " --> pdb=" O LEU F1276 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER F1280 " --> pdb=" O HIS F1277 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER F1281 " --> pdb=" O VAL F1278 " (cutoff:3.500A) Processing helix chain 'F' and resid 1292 through 1299 Proline residue: F1296 - end of helix removed outlier: 4.284A pdb=" N SER F1299 " --> pdb=" O LEU F1295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1292 through 1299' Processing helix chain 'F' and resid 1312 through 1328 Processing helix chain 'F' and resid 1336 through 1339 No H-bonds generated for 'chain 'F' and resid 1336 through 1339' Processing helix chain 'F' and resid 1341 through 1365 Processing helix chain 'F' and resid 1380 through 1393 Processing helix chain 'F' and resid 1397 through 1406 Processing helix chain 'F' and resid 1410 through 1422 removed outlier: 4.023A pdb=" N CYS F1420 " --> pdb=" O TYR F1416 " (cutoff:3.500A) Processing helix chain 'F' and resid 1429 through 1445 removed outlier: 3.662A pdb=" N GLY F1432 " --> pdb=" O ASN F1429 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN F1433 " --> pdb=" O GLN F1430 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN F1437 " --> pdb=" O LEU F1434 " (cutoff:3.500A) Processing helix chain 'F' and resid 1448 through 1456 Processing helix chain 'F' and resid 1463 through 1468 removed outlier: 5.161A pdb=" N GLU F1468 " --> pdb=" O VAL F1464 " (cutoff:3.500A) Processing helix chain 'F' and resid 1476 through 1489 removed outlier: 3.554A pdb=" N LYS F1488 " --> pdb=" O ASN F1484 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE F1489 " --> pdb=" O VAL F1485 " (cutoff:3.500A) Processing helix chain 'F' and resid 1493 through 1504 Processing helix chain 'F' and resid 1509 through 1514 Processing helix chain 'F' and resid 1533 through 1544 removed outlier: 4.844A pdb=" N GLU F1540 " --> pdb=" O SER F1536 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA F1541 " --> pdb=" O ILE F1537 " (cutoff:3.500A) Processing helix chain 'F' and resid 1549 through 1560 removed outlier: 4.434A pdb=" N SER F1560 " --> pdb=" O GLU F1556 " (cutoff:3.500A) Processing helix chain 'F' and resid 1567 through 1583 Processing helix chain 'F' and resid 1587 through 1604 Processing helix chain 'F' and resid 1618 through 1634 removed outlier: 4.193A pdb=" N LYS F1623 " --> pdb=" O ASN F1619 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU F1633 " --> pdb=" O ASP F1629 " (cutoff:3.500A) Processing helix chain 'F' and resid 1639 through 1655 Processing helix chain 'F' and resid 1660 through 1676 Processing helix chain 'F' and resid 1680 through 1700 Processing helix chain 'F' and resid 1705 through 1714 removed outlier: 5.021A pdb=" N HIS F1712 " --> pdb=" O GLU F1708 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS F1713 " --> pdb=" O SER F1709 " (cutoff:3.500A) Processing helix chain 'F' and resid 1719 through 1732 Processing helix chain 'F' and resid 1735 through 1748 Processing helix chain 'F' and resid 1759 through 1774 Processing helix chain 'F' and resid 1780 through 1792 removed outlier: 3.891A pdb=" N GLN F1785 " --> pdb=" O GLN F1781 " (cutoff:3.500A) Processing helix chain 'F' and resid 1798 through 1817 removed outlier: 3.870A pdb=" N GLU F1817 " --> pdb=" O ARG F1813 " (cutoff:3.500A) Processing helix chain 'F' and resid 1824 through 1838 removed outlier: 3.948A pdb=" N GLU F1838 " --> pdb=" O LEU F1834 " (cutoff:3.500A) Processing helix chain 'F' and resid 1844 through 1864 Proline residue: F1849 - end of helix removed outlier: 5.040A pdb=" N PHE F1854 " --> pdb=" O LYS F1850 " (cutoff:3.500A) Processing helix chain 'F' and resid 1875 through 1891 removed outlier: 3.790A pdb=" N HIS F1891 " --> pdb=" O GLU F1887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1895 through 1905 removed outlier: 3.839A pdb=" N TYR F1898 " --> pdb=" O TYR F1895 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE F1899 " --> pdb=" O ILE F1896 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL F1900 " --> pdb=" O TRP F1897 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR F1902 " --> pdb=" O PHE F1899 " (cutoff:3.500A) Processing helix chain 'F' and resid 1914 through 1928 Processing helix chain 'F' and resid 1932 through 1941 removed outlier: 3.716A pdb=" N LEU F1935 " --> pdb=" O SER F1932 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TRP F1936 " --> pdb=" O HIS F1933 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F1939 " --> pdb=" O TRP F1936 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU F1941 " --> pdb=" O ILE F1938 " (cutoff:3.500A) Processing helix chain 'F' and resid 1949 through 1962 removed outlier: 4.498A pdb=" N ILE F1956 " --> pdb=" O ARG F1952 " (cutoff:3.500A) Processing helix chain 'F' and resid 1970 through 1983 Processing helix chain 'F' and resid 2086 through 2103 removed outlier: 4.391A pdb=" N PHE F2099 " --> pdb=" O THR F2095 " (cutoff:3.500A) Processing helix chain 'F' and resid 2138 through 2148 Processing helix chain 'F' and resid 2158 through 2163 Processing helix chain 'F' and resid 2168 through 2180 removed outlier: 4.219A pdb=" N GLU F2172 " --> pdb=" O ASP F2168 " (cutoff:3.500A) Processing helix chain 'F' and resid 2185 through 2192 removed outlier: 4.400A pdb=" N LEU F2190 " --> pdb=" O GLN F2187 " (cutoff:3.500A) Processing helix chain 'F' and resid 2196 through 2220 removed outlier: 4.128A pdb=" N MET F2213 " --> pdb=" O SER F2209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS F2218 " --> pdb=" O ALA F2214 " (cutoff:3.500A) Processing helix chain 'F' and resid 2266 through 2272 removed outlier: 4.584A pdb=" N ASP F2270 " --> pdb=" O ASN F2267 " (cutoff:3.500A) Processing helix chain 'F' and resid 2280 through 2292 Processing helix chain 'F' and resid 2296 through 2304 Processing helix chain 'F' and resid 2317 through 2328 Processing helix chain 'F' and resid 2341 through 2351 Processing helix chain 'F' and resid 2354 through 2358 Processing helix chain 'F' and resid 2362 through 2364 No H-bonds generated for 'chain 'F' and resid 2362 through 2364' Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 250 through 264 removed outlier: 3.666A pdb=" N LYS C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 286 Processing helix chain 'C' and resid 294 through 309 removed outlier: 4.520A pdb=" N PHE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 356 through 381 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 434 removed outlier: 3.524A pdb=" N VAL C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 447 through 461 removed outlier: 4.005A pdb=" N THR C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.521A pdb=" N SER C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 536 through 562 Processing helix chain 'C' and resid 573 through 592 removed outlier: 4.272A pdb=" N SER C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 621 removed outlier: 3.915A pdb=" N ILE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 609 " --> pdb=" O CYS C 605 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.686A pdb=" N LYS C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 removed outlier: 3.808A pdb=" N PHE C 645 " --> pdb=" O SER C 641 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N CYS C 648 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 649 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 667 removed outlier: 3.690A pdb=" N ASP C 662 " --> pdb=" O ARG C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 680 Processing helix chain 'C' and resid 693 through 709 removed outlier: 4.989A pdb=" N ASN C 702 " --> pdb=" O LYS C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 725 removed outlier: 3.782A pdb=" N ILE C 724 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 725 " --> pdb=" O ALA C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 742 removed outlier: 3.504A pdb=" N ASP C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 222 through 228 Processing helix chain 'D' and resid 250 through 264 removed outlier: 3.616A pdb=" N LYS D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 286 Processing helix chain 'D' and resid 294 through 309 removed outlier: 4.516A pdb=" N PHE D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 332 Processing helix chain 'D' and resid 356 through 381 Processing helix chain 'D' and resid 393 through 406 Processing helix chain 'D' and resid 415 through 434 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 447 through 461 removed outlier: 4.016A pdb=" N THR D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG D 456 " --> pdb=" O ASP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 536 through 562 Processing helix chain 'D' and resid 573 through 592 removed outlier: 4.255A pdb=" N SER D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 621 removed outlier: 3.947A pdb=" N ILE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 609 " --> pdb=" O CYS D 605 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 625 No H-bonds generated for 'chain 'D' and resid 623 through 625' Processing helix chain 'D' and resid 628 through 633 removed outlier: 3.712A pdb=" N LYS D 632 " --> pdb=" O GLU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 removed outlier: 3.721A pdb=" N PHE D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 666 removed outlier: 3.724A pdb=" N ASP D 662 " --> pdb=" O ARG D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 680 Processing helix chain 'D' and resid 694 through 709 removed outlier: 3.556A pdb=" N MET D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN D 702 " --> pdb=" O LYS D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 725 removed outlier: 3.700A pdb=" N ILE D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 725 " --> pdb=" O ALA D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 742 removed outlier: 3.568A pdb=" N ASP D 739 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 17 removed outlier: 3.660A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.940A pdb=" N ASN E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 83 removed outlier: 3.748A pdb=" N LEU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.711A pdb=" N ASP E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.662A pdb=" N MET E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 139 through 160 removed outlier: 4.255A pdb=" N LYS E 143 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE E 144 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR E 147 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA E 148 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE E 150 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET E 154 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 158 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 172 through 188 removed outlier: 3.782A pdb=" N PHE E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 228 removed outlier: 3.528A pdb=" N ASN E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.559A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 244 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 284 removed outlier: 3.609A pdb=" N ASN E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 305 Processing helix chain 'E' and resid 310 through 318 removed outlier: 3.881A pdb=" N LYS E 313 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS E 318 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 354 Processing helix chain 'E' and resid 391 through 405 removed outlier: 4.480A pdb=" N PHE E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN E 405 " --> pdb=" O LEU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.670A pdb=" N LEU E 436 " --> pdb=" O PHE E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 471 removed outlier: 3.597A pdb=" N CYS E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 503 No H-bonds generated for 'chain 'E' and resid 501 through 503' Processing helix chain 'E' and resid 512 through 515 No H-bonds generated for 'chain 'E' and resid 512 through 515' Processing helix chain 'E' and resid 517 through 528 removed outlier: 3.840A pdb=" N LEU E 527 " --> pdb=" O HIS E 523 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 552 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 582 through 588 Processing helix chain 'E' and resid 592 through 595 No H-bonds generated for 'chain 'E' and resid 592 through 595' Processing helix chain 'E' and resid 606 through 617 removed outlier: 4.139A pdb=" N SER E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 637 removed outlier: 3.576A pdb=" N LYS E 624 " --> pdb=" O PRO E 621 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 625 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN E 626 " --> pdb=" O VAL E 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 629 " --> pdb=" O ASN E 626 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN E 633 " --> pdb=" O ALA E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 654 removed outlier: 3.839A pdb=" N ILE E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 675 Processing helix chain 'E' and resid 680 through 695 Proline residue: E 686 - end of helix Proline residue: E 689 - end of helix removed outlier: 3.954A pdb=" N ARG E 693 " --> pdb=" O PRO E 689 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN E 694 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 695 " --> pdb=" O LEU E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 713 Processing helix chain 'E' and resid 717 through 727 removed outlier: 4.494A pdb=" N ILE E 723 " --> pdb=" O THR E 719 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG E 726 " --> pdb=" O ASP E 722 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR E 727 " --> pdb=" O ILE E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 733 removed outlier: 4.177A pdb=" N ILE E 733 " --> pdb=" O PRO E 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 748 Processing helix chain 'E' and resid 756 through 766 Processing helix chain 'E' and resid 769 through 777 Processing helix chain 'E' and resid 784 through 792 Processing helix chain 'E' and resid 806 through 808 No H-bonds generated for 'chain 'E' and resid 806 through 808' Processing helix chain 'E' and resid 810 through 816 Processing helix chain 'E' and resid 828 through 842 Processing helix chain 'E' and resid 845 through 847 No H-bonds generated for 'chain 'E' and resid 845 through 847' Processing helix chain 'E' and resid 861 through 863 No H-bonds generated for 'chain 'E' and resid 861 through 863' Processing helix chain 'E' and resid 869 through 891 removed outlier: 4.443A pdb=" N LEU E 881 " --> pdb=" O GLN E 877 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY E 882 " --> pdb=" O ASP E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 915 Processing helix chain 'E' and resid 919 through 924 Processing helix chain 'E' and resid 928 through 938 Processing helix chain 'E' and resid 943 through 955 Processing helix chain 'E' and resid 963 through 965 No H-bonds generated for 'chain 'E' and resid 963 through 965' Processing helix chain 'E' and resid 967 through 979 removed outlier: 6.886A pdb=" N SER E 978 " --> pdb=" O LEU E 974 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU E 979 " --> pdb=" O GLN E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 998 Processing helix chain 'E' and resid 1000 through 1003 No H-bonds generated for 'chain 'E' and resid 1000 through 1003' Processing helix chain 'E' and resid 1008 through 1016 Processing helix chain 'E' and resid 1022 through 1025 No H-bonds generated for 'chain 'E' and resid 1022 through 1025' Processing helix chain 'E' and resid 1028 through 1038 removed outlier: 4.130A pdb=" N ARG E1031 " --> pdb=" O GLN E1028 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E1037 " --> pdb=" O ASN E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1051 removed outlier: 3.953A pdb=" N LYS E1051 " --> pdb=" O ALA E1047 " (cutoff:3.500A) Processing helix chain 'E' and resid 1055 through 1075 Processing helix chain 'E' and resid 1091 through 1104 Processing helix chain 'E' and resid 1110 through 1123 Processing helix chain 'E' and resid 1149 through 1164 Processing helix chain 'E' and resid 1174 through 1190 Processing helix chain 'E' and resid 1207 through 1214 Processing helix chain 'E' and resid 1218 through 1227 removed outlier: 3.699A pdb=" N TYR E1225 " --> pdb=" O LYS E1221 " (cutoff:3.500A) Proline residue: E1226 - end of helix Processing helix chain 'E' and resid 1246 through 1251 Processing helix chain 'E' and resid 1257 through 1267 Processing helix chain 'E' and resid 1275 through 1281 removed outlier: 3.761A pdb=" N PHE E1279 " --> pdb=" O LEU E1276 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E1280 " --> pdb=" O HIS E1277 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER E1281 " --> pdb=" O VAL E1278 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1299 Proline residue: E1296 - end of helix removed outlier: 4.284A pdb=" N SER E1299 " --> pdb=" O LEU E1295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1292 through 1299' Processing helix chain 'E' and resid 1312 through 1328 Processing helix chain 'E' and resid 1336 through 1339 No H-bonds generated for 'chain 'E' and resid 1336 through 1339' Processing helix chain 'E' and resid 1341 through 1365 Processing helix chain 'E' and resid 1380 through 1393 Processing helix chain 'E' and resid 1397 through 1406 Processing helix chain 'E' and resid 1410 through 1422 removed outlier: 4.023A pdb=" N CYS E1420 " --> pdb=" O TYR E1416 " (cutoff:3.500A) Processing helix chain 'E' and resid 1429 through 1445 removed outlier: 3.662A pdb=" N GLY E1432 " --> pdb=" O ASN E1429 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN E1433 " --> pdb=" O GLN E1430 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN E1437 " --> pdb=" O LEU E1434 " (cutoff:3.500A) Processing helix chain 'E' and resid 1448 through 1456 Processing helix chain 'E' and resid 1463 through 1468 removed outlier: 5.161A pdb=" N GLU E1468 " --> pdb=" O VAL E1464 " (cutoff:3.500A) Processing helix chain 'E' and resid 1476 through 1489 removed outlier: 3.554A pdb=" N LYS E1488 " --> pdb=" O ASN E1484 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE E1489 " --> pdb=" O VAL E1485 " (cutoff:3.500A) Processing helix chain 'E' and resid 1493 through 1504 Processing helix chain 'E' and resid 1509 through 1514 Processing helix chain 'E' and resid 1533 through 1544 removed outlier: 4.844A pdb=" N GLU E1540 " --> pdb=" O SER E1536 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA E1541 " --> pdb=" O ILE E1537 " (cutoff:3.500A) Processing helix chain 'E' and resid 1549 through 1560 removed outlier: 4.434A pdb=" N SER E1560 " --> pdb=" O GLU E1556 " (cutoff:3.500A) Processing helix chain 'E' and resid 1567 through 1583 Processing helix chain 'E' and resid 1587 through 1604 Processing helix chain 'E' and resid 1618 through 1634 removed outlier: 4.193A pdb=" N LYS E1623 " --> pdb=" O ASN E1619 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU E1633 " --> pdb=" O ASP E1629 " (cutoff:3.500A) Processing helix chain 'E' and resid 1639 through 1655 Processing helix chain 'E' and resid 1660 through 1676 Processing helix chain 'E' and resid 1680 through 1700 Processing helix chain 'E' and resid 1705 through 1714 removed outlier: 5.021A pdb=" N HIS E1712 " --> pdb=" O GLU E1708 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS E1713 " --> pdb=" O SER E1709 " (cutoff:3.500A) Processing helix chain 'E' and resid 1719 through 1732 Processing helix chain 'E' and resid 1735 through 1748 Processing helix chain 'E' and resid 1759 through 1774 Processing helix chain 'E' and resid 1780 through 1792 removed outlier: 3.892A pdb=" N GLN E1785 " --> pdb=" O GLN E1781 " (cutoff:3.500A) Processing helix chain 'E' and resid 1798 through 1817 removed outlier: 3.870A pdb=" N GLU E1817 " --> pdb=" O ARG E1813 " (cutoff:3.500A) Processing helix chain 'E' and resid 1824 through 1838 removed outlier: 3.947A pdb=" N GLU E1838 " --> pdb=" O LEU E1834 " (cutoff:3.500A) Processing helix chain 'E' and resid 1844 through 1864 Proline residue: E1849 - end of helix removed outlier: 5.040A pdb=" N PHE E1854 " --> pdb=" O LYS E1850 " (cutoff:3.500A) Processing helix chain 'E' and resid 1875 through 1891 removed outlier: 3.789A pdb=" N HIS E1891 " --> pdb=" O GLU E1887 " (cutoff:3.500A) Processing helix chain 'E' and resid 1895 through 1905 removed outlier: 3.839A pdb=" N TYR E1898 " --> pdb=" O TYR E1895 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE E1899 " --> pdb=" O ILE E1896 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E1900 " --> pdb=" O TRP E1897 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR E1902 " --> pdb=" O PHE E1899 " (cutoff:3.500A) Processing helix chain 'E' and resid 1914 through 1928 Processing helix chain 'E' and resid 1932 through 1941 removed outlier: 3.716A pdb=" N LEU E1935 " --> pdb=" O SER E1932 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TRP E1936 " --> pdb=" O HIS E1933 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E1939 " --> pdb=" O TRP E1936 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E1941 " --> pdb=" O ILE E1938 " (cutoff:3.500A) Processing helix chain 'E' and resid 1949 through 1962 removed outlier: 4.497A pdb=" N ILE E1956 " --> pdb=" O ARG E1952 " (cutoff:3.500A) Processing helix chain 'E' and resid 1970 through 1983 Processing helix chain 'E' and resid 2086 through 2103 removed outlier: 4.391A pdb=" N PHE E2099 " --> pdb=" O THR E2095 " (cutoff:3.500A) Processing helix chain 'E' and resid 2138 through 2148 Processing helix chain 'E' and resid 2158 through 2163 Processing helix chain 'E' and resid 2168 through 2180 removed outlier: 4.220A pdb=" N GLU E2172 " --> pdb=" O ASP E2168 " (cutoff:3.500A) Processing helix chain 'E' and resid 2185 through 2192 removed outlier: 4.400A pdb=" N LEU E2190 " --> pdb=" O GLN E2187 " (cutoff:3.500A) Processing helix chain 'E' and resid 2196 through 2220 removed outlier: 4.128A pdb=" N MET E2213 " --> pdb=" O SER E2209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E2218 " --> pdb=" O ALA E2214 " (cutoff:3.500A) Processing helix chain 'E' and resid 2266 through 2272 removed outlier: 4.584A pdb=" N ASP E2270 " --> pdb=" O ASN E2267 " (cutoff:3.500A) Processing helix chain 'E' and resid 2280 through 2292 Processing helix chain 'E' and resid 2296 through 2304 Processing helix chain 'E' and resid 2317 through 2328 Processing helix chain 'E' and resid 2341 through 2351 Processing helix chain 'E' and resid 2354 through 2358 Processing helix chain 'E' and resid 2362 through 2364 No H-bonds generated for 'chain 'E' and resid 2362 through 2364' Processing sheet with id= A, first strand: chain 'F' and resid 2064 through 2068 removed outlier: 4.245A pdb=" N GLY F2076 " --> pdb=" O MET F2131 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE F2128 " --> pdb=" O SER F2121 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER F2121 " --> pdb=" O ILE F2128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLU F2130 " --> pdb=" O VAL F2119 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL F2119 " --> pdb=" O GLU F2130 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 2230 through 2232 Processing sheet with id= C, first strand: chain 'E' and resid 2064 through 2068 removed outlier: 4.245A pdb=" N GLY E2076 " --> pdb=" O MET E2131 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE E2128 " --> pdb=" O SER E2121 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER E2121 " --> pdb=" O ILE E2128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLU E2130 " --> pdb=" O VAL E2119 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL E2119 " --> pdb=" O GLU E2130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 2230 through 2232 2125 hydrogen bonds defined for protein. 5985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.63 Time building geometry restraints manager: 18.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10367 1.33 - 1.45: 10060 1.45 - 1.57: 26335 1.57 - 1.69: 12 1.69 - 1.81: 308 Bond restraints: 47082 Sorted by residual: bond pdb=" O3A ANP E2401 " pdb=" PB ANP E2401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP F2401 " pdb=" PB ANP F2401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" N3B ANP E2401 " pdb=" PG ANP E2401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N3B ANP F2401 " pdb=" PG ANP F2401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N PHE F1293 " pdb=" CA PHE F1293 " ideal model delta sigma weight residual 1.459 1.402 0.057 1.20e-02 6.94e+03 2.28e+01 ... (remaining 47077 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.52: 557 104.52 - 111.94: 21446 111.94 - 119.35: 18051 119.35 - 126.76: 23122 126.76 - 134.18: 611 Bond angle restraints: 63787 Sorted by residual: angle pdb=" N PHE E1293 " pdb=" CA PHE E1293 " pdb=" C PHE E1293 " ideal model delta sigma weight residual 111.14 100.52 10.62 1.08e+00 8.57e-01 9.68e+01 angle pdb=" N PHE F1293 " pdb=" CA PHE F1293 " pdb=" C PHE F1293 " ideal model delta sigma weight residual 111.14 100.53 10.61 1.08e+00 8.57e-01 9.65e+01 angle pdb=" C PHE F1293 " pdb=" N LEU F1294 " pdb=" CA LEU F1294 " ideal model delta sigma weight residual 120.28 109.24 11.04 1.34e+00 5.57e-01 6.78e+01 angle pdb=" C PHE E1293 " pdb=" N LEU E1294 " pdb=" CA LEU E1294 " ideal model delta sigma weight residual 120.28 109.25 11.03 1.34e+00 5.57e-01 6.78e+01 angle pdb=" PB ANP E2401 " pdb=" N3B ANP E2401 " pdb=" PG ANP E2401 " ideal model delta sigma weight residual 126.95 106.65 20.30 3.00e+00 1.11e-01 4.58e+01 ... (remaining 63782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 28111 35.96 - 71.91: 312 71.91 - 107.87: 12 107.87 - 143.82: 0 143.82 - 179.78: 2 Dihedral angle restraints: 28437 sinusoidal: 11421 harmonic: 17016 Sorted by residual: dihedral pdb=" CD BARG D 228 " pdb=" NE BARG D 228 " pdb=" CZ BARG D 228 " pdb=" NH1BARG D 228 " ideal model delta sinusoidal sigma weight residual 0.00 179.78 -179.78 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG C 228 " pdb=" NE BARG C 228 " pdb=" CZ BARG C 228 " pdb=" NH1BARG C 228 " ideal model delta sinusoidal sigma weight residual 0.00 179.76 -179.76 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA SER F1754 " pdb=" C SER F1754 " pdb=" N VAL F1755 " pdb=" CA VAL F1755 " ideal model delta harmonic sigma weight residual -180.00 -124.48 -55.52 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 28434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 6555 0.099 - 0.199: 732 0.199 - 0.298: 49 0.298 - 0.398: 4 0.398 - 0.497: 2 Chirality restraints: 7342 Sorted by residual: chirality pdb=" CG LEU F1739 " pdb=" CB LEU F1739 " pdb=" CD1 LEU F1739 " pdb=" CD2 LEU F1739 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CG LEU E1739 " pdb=" CB LEU E1739 " pdb=" CD1 LEU E1739 " pdb=" CD2 LEU E1739 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CG LEU E2268 " pdb=" CB LEU E2268 " pdb=" CD1 LEU E2268 " pdb=" CD2 LEU E2268 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 7339 not shown) Planarity restraints: 8019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C VAL C 470 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR C 471 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 470 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL D 470 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL D 470 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR D 471 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 770 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" CD GLN F 770 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLN F 770 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN F 770 " 0.019 2.00e-02 2.50e+03 ... (remaining 8016 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 91 2.32 - 2.97: 21391 2.97 - 3.61: 76982 3.61 - 4.26: 113731 4.26 - 4.90: 178120 Nonbonded interactions: 390315 Sorted by model distance: nonbonded pdb=" O ASN F1292 " pdb=" CD PRO F1296 " model vdw 1.678 3.440 nonbonded pdb=" O ASN E1292 " pdb=" CD PRO E1296 " model vdw 1.678 3.440 nonbonded pdb=" NZ LYS F1259 " pdb=" OG SER F1291 " model vdw 1.785 2.520 nonbonded pdb=" NZ LYS E1259 " pdb=" OG SER E1291 " model vdw 1.786 2.520 nonbonded pdb=" O SER F1291 " pdb=" N LEU F1295 " model vdw 2.094 2.520 ... (remaining 390310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 189 through 227 or resid 229 through 747)) selection = (chain 'D' and (resid 189 through 227 or resid 229 through 550 or (resid 551 and \ (name N or name CA or name C or name O or name CB )) or resid 552 through 747)) \ } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.040 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 130.720 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.145 47082 Z= 0.446 Angle : 1.246 20.295 63787 Z= 0.651 Chirality : 0.063 0.497 7342 Planarity : 0.008 0.076 8019 Dihedral : 12.663 179.776 17361 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.07 % Favored : 88.84 % Rotamer: Outliers : 1.08 % Allowed : 8.12 % Favored : 90.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.09), residues: 5688 helix: -2.55 (0.07), residues: 3606 sheet: -2.64 (0.44), residues: 74 loop : -3.54 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP D 643 HIS 0.025 0.003 HIS D 665 PHE 0.052 0.004 PHE F1046 TYR 0.031 0.003 TYR E1786 ARG 0.031 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1552 time to evaluate : 5.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 55 LEU cc_start: 0.8657 (pt) cc_final: 0.8440 (pt) REVERT: F 120 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8584 (tp) REVERT: F 123 MET cc_start: 0.9130 (mtp) cc_final: 0.8909 (mtp) REVERT: F 154 MET cc_start: 0.8301 (ttp) cc_final: 0.7986 (tmm) REVERT: F 186 TYR cc_start: 0.9039 (t80) cc_final: 0.8728 (t80) REVERT: F 194 THR cc_start: 0.8391 (m) cc_final: 0.7997 (m) REVERT: F 295 MET cc_start: 0.9029 (tpt) cc_final: 0.8349 (ptt) REVERT: F 318 HIS cc_start: 0.8893 (m-70) cc_final: 0.8620 (m-70) REVERT: F 345 ILE cc_start: 0.9042 (mt) cc_final: 0.8837 (mm) REVERT: F 347 TYR cc_start: 0.8975 (t80) cc_final: 0.8654 (t80) REVERT: F 392 GLN cc_start: 0.7655 (mt0) cc_final: 0.7217 (mm-40) REVERT: F 441 VAL cc_start: 0.9501 (p) cc_final: 0.9281 (m) REVERT: F 540 LEU cc_start: 0.9537 (mt) cc_final: 0.9249 (mt) REVERT: F 549 ARG cc_start: 0.9274 (mtt-85) cc_final: 0.8762 (tpp80) REVERT: F 579 ASN cc_start: 0.8202 (t0) cc_final: 0.7837 (t0) REVERT: F 587 LEU cc_start: 0.9125 (tt) cc_final: 0.8665 (mm) REVERT: F 636 LEU cc_start: 0.9600 (mt) cc_final: 0.9367 (mt) REVERT: F 667 LEU cc_start: 0.8621 (tm) cc_final: 0.8413 (tm) REVERT: F 668 GLN cc_start: 0.8685 (mm110) cc_final: 0.8417 (mm110) REVERT: F 671 ASN cc_start: 0.8912 (m110) cc_final: 0.8512 (m-40) REVERT: F 691 LEU cc_start: 0.9060 (tp) cc_final: 0.8741 (mt) REVERT: F 907 ILE cc_start: 0.9455 (mt) cc_final: 0.9168 (mt) REVERT: F 928 GLN cc_start: 0.9025 (pm20) cc_final: 0.8529 (pt0) REVERT: F 950 TRP cc_start: 0.7811 (m100) cc_final: 0.6810 (m100) REVERT: F 1108 LEU cc_start: 0.8104 (tm) cc_final: 0.7774 (tm) REVERT: F 1118 LYS cc_start: 0.9345 (ptpt) cc_final: 0.8833 (ptpp) REVERT: F 1126 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7341 (tm) REVERT: F 1314 ASP cc_start: 0.9462 (t0) cc_final: 0.9098 (m-30) REVERT: F 1353 PHE cc_start: 0.9062 (m-10) cc_final: 0.8794 (m-80) REVERT: F 1503 MET cc_start: 0.8805 (ttp) cc_final: 0.8423 (tpp) REVERT: F 1510 SER cc_start: 0.9407 (m) cc_final: 0.9193 (p) REVERT: F 1512 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8190 (mp) REVERT: F 1550 THR cc_start: 0.9183 (m) cc_final: 0.8820 (m) REVERT: F 1628 TYR cc_start: 0.8649 (t80) cc_final: 0.8420 (t80) REVERT: F 1651 TYR cc_start: 0.8539 (t80) cc_final: 0.8209 (t80) REVERT: F 1666 ILE cc_start: 0.9050 (pp) cc_final: 0.8793 (pp) REVERT: F 1691 PHE cc_start: 0.9252 (t80) cc_final: 0.8920 (t80) REVERT: F 1696 LEU cc_start: 0.9469 (pp) cc_final: 0.9252 (pp) REVERT: F 1720 GLN cc_start: 0.8098 (pm20) cc_final: 0.7847 (pm20) REVERT: F 1837 PHE cc_start: 0.8704 (m-10) cc_final: 0.8495 (m-80) REVERT: F 1920 MET cc_start: 0.9253 (mtm) cc_final: 0.9047 (ppp) REVERT: F 1937 TYR cc_start: 0.8989 (m-80) cc_final: 0.8789 (m-80) REVERT: F 1955 HIS cc_start: 0.8824 (t70) cc_final: 0.8621 (t-170) REVERT: F 2110 ARG cc_start: 0.8588 (ttm110) cc_final: 0.7597 (tpt170) REVERT: F 2161 ARG cc_start: 0.9176 (ptm160) cc_final: 0.8338 (ptp90) REVERT: F 2282 LYS cc_start: 0.9146 (tttm) cc_final: 0.8928 (mtpt) REVERT: F 2295 ASN cc_start: 0.9166 (p0) cc_final: 0.8955 (t0) REVERT: F 2301 ASN cc_start: 0.8660 (m-40) cc_final: 0.8408 (m110) REVERT: F 2364 TRP cc_start: 0.8569 (t60) cc_final: 0.8180 (t60) REVERT: C 201 ASP cc_start: 0.8313 (t0) cc_final: 0.8064 (t0) REVERT: C 210 ILE cc_start: 0.9282 (mt) cc_final: 0.9051 (mt) REVERT: C 220 LEU cc_start: 0.7917 (mt) cc_final: 0.7609 (mp) REVERT: C 257 LEU cc_start: 0.9374 (tp) cc_final: 0.8564 (tp) REVERT: C 269 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8824 (mtp85) REVERT: C 278 ILE cc_start: 0.9647 (mt) cc_final: 0.9289 (tp) REVERT: C 303 MET cc_start: 0.8742 (ttm) cc_final: 0.8509 (ttm) REVERT: C 328 ASP cc_start: 0.8731 (p0) cc_final: 0.8526 (m-30) REVERT: C 377 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8107 (mtp85) REVERT: C 417 VAL cc_start: 0.8905 (m) cc_final: 0.8435 (m) REVERT: C 431 ILE cc_start: 0.9208 (pt) cc_final: 0.8869 (pt) REVERT: C 435 MET cc_start: 0.6736 (ptp) cc_final: 0.6499 (ptt) REVERT: C 437 ASN cc_start: 0.8169 (t0) cc_final: 0.7966 (p0) REVERT: C 518 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8232 (ttt180) REVERT: C 540 LYS cc_start: 0.9389 (ptpp) cc_final: 0.9163 (ptpp) REVERT: C 547 LYS cc_start: 0.9188 (mttt) cc_final: 0.8833 (mttp) REVERT: C 558 ASN cc_start: 0.8959 (m-40) cc_final: 0.8545 (t0) REVERT: C 562 ILE cc_start: 0.8081 (mt) cc_final: 0.7661 (mt) REVERT: C 591 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8421 (mt-10) REVERT: C 654 THR cc_start: 0.6384 (p) cc_final: 0.5807 (p) REVERT: C 660 MET cc_start: 0.9097 (mtp) cc_final: 0.8648 (mmm) REVERT: C 664 ARG cc_start: 0.8992 (ptt180) cc_final: 0.8737 (ppt170) REVERT: C 700 GLN cc_start: 0.8635 (pp30) cc_final: 0.8118 (pp30) REVERT: C 707 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7898 (tmm160) REVERT: D 220 LEU cc_start: 0.7740 (mt) cc_final: 0.7531 (mt) REVERT: D 231 LEU cc_start: 0.7359 (pt) cc_final: 0.7084 (mt) REVERT: D 256 SER cc_start: 0.9201 (t) cc_final: 0.7355 (p) REVERT: D 257 LEU cc_start: 0.9390 (tp) cc_final: 0.8414 (tp) REVERT: D 269 ARG cc_start: 0.8996 (mtp180) cc_final: 0.8728 (mtp85) REVERT: D 278 ILE cc_start: 0.9641 (mt) cc_final: 0.9213 (tp) REVERT: D 303 MET cc_start: 0.8760 (ttm) cc_final: 0.8512 (ttm) REVERT: D 328 ASP cc_start: 0.8720 (p0) cc_final: 0.8512 (m-30) REVERT: D 431 ILE cc_start: 0.9171 (pt) cc_final: 0.8903 (pt) REVERT: D 462 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8055 (mt-10) REVERT: D 540 LYS cc_start: 0.9409 (ptpp) cc_final: 0.9099 (ptpp) REVERT: D 547 LYS cc_start: 0.9226 (mttt) cc_final: 0.8681 (mttp) REVERT: D 558 ASN cc_start: 0.8875 (m-40) cc_final: 0.8415 (t0) REVERT: D 562 ILE cc_start: 0.8045 (mt) cc_final: 0.7655 (mt) REVERT: D 654 THR cc_start: 0.5696 (p) cc_final: 0.5292 (p) REVERT: D 662 ASP cc_start: 0.8208 (m-30) cc_final: 0.7985 (m-30) REVERT: D 664 ARG cc_start: 0.9039 (ptt180) cc_final: 0.8510 (ppt170) REVERT: D 720 MET cc_start: 0.7896 (mtm) cc_final: 0.7136 (ptp) REVERT: E 55 LEU cc_start: 0.8721 (pt) cc_final: 0.8426 (pt) REVERT: E 120 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8147 (pp) REVERT: E 123 MET cc_start: 0.9147 (mtp) cc_final: 0.8592 (ptt) REVERT: E 126 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7598 (tppt) REVERT: E 154 MET cc_start: 0.8369 (ttp) cc_final: 0.8125 (tmm) REVERT: E 186 TYR cc_start: 0.9061 (t80) cc_final: 0.8361 (t80) REVERT: E 295 MET cc_start: 0.9126 (tpt) cc_final: 0.8728 (ptt) REVERT: E 318 HIS cc_start: 0.8720 (m-70) cc_final: 0.7857 (m90) REVERT: E 458 TRP cc_start: 0.8516 (m100) cc_final: 0.8088 (m100) REVERT: E 545 PHE cc_start: 0.9142 (m-80) cc_final: 0.8917 (m-80) REVERT: E 549 ARG cc_start: 0.9368 (mtt-85) cc_final: 0.8833 (tpp80) REVERT: E 551 PHE cc_start: 0.9004 (m-10) cc_final: 0.8588 (m-80) REVERT: E 579 ASN cc_start: 0.8308 (t0) cc_final: 0.7734 (t0) REVERT: E 587 LEU cc_start: 0.9194 (tt) cc_final: 0.8745 (mm) REVERT: E 592 ILE cc_start: 0.9696 (mt) cc_final: 0.9460 (mt) REVERT: E 631 TRP cc_start: 0.8879 (m100) cc_final: 0.8658 (m100) REVERT: E 668 GLN cc_start: 0.8741 (mm110) cc_final: 0.8420 (mm-40) REVERT: E 691 LEU cc_start: 0.9290 (tp) cc_final: 0.9050 (mt) REVERT: E 727 TYR cc_start: 0.8015 (m-80) cc_final: 0.7521 (m-80) REVERT: E 747 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8903 (pt) REVERT: E 835 ASN cc_start: 0.9336 (m110) cc_final: 0.9136 (p0) REVERT: E 902 GLU cc_start: 0.8391 (mp0) cc_final: 0.8035 (pt0) REVERT: E 907 ILE cc_start: 0.9497 (mt) cc_final: 0.9286 (mt) REVERT: E 928 GLN cc_start: 0.8868 (pm20) cc_final: 0.8562 (pt0) REVERT: E 955 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7850 (mtt-85) REVERT: E 1056 TYR cc_start: 0.8008 (m-80) cc_final: 0.7762 (m-80) REVERT: E 1100 ASP cc_start: 0.9370 (p0) cc_final: 0.8906 (t0) REVERT: E 1109 ASP cc_start: 0.8161 (t0) cc_final: 0.7899 (p0) REVERT: E 1118 LYS cc_start: 0.9394 (ptpt) cc_final: 0.8879 (ptpp) REVERT: E 1126 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7053 (tm) REVERT: E 1178 LEU cc_start: 0.8492 (mm) cc_final: 0.8291 (mm) REVERT: E 1212 LEU cc_start: 0.8441 (mt) cc_final: 0.8224 (mp) REVERT: E 1314 ASP cc_start: 0.9403 (t0) cc_final: 0.8957 (m-30) REVERT: E 1476 TRP cc_start: 0.8559 (p90) cc_final: 0.7445 (p90) REVERT: E 1503 MET cc_start: 0.8871 (ttp) cc_final: 0.8353 (tpp) REVERT: E 1510 SER cc_start: 0.9283 (m) cc_final: 0.9063 (p) REVERT: E 1512 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8024 (mp) REVERT: E 1543 ASN cc_start: 0.9028 (m110) cc_final: 0.8678 (m110) REVERT: E 1550 THR cc_start: 0.9265 (m) cc_final: 0.8789 (m) REVERT: E 1564 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 1573 TYR cc_start: 0.7345 (t80) cc_final: 0.7119 (t80) REVERT: E 1651 TYR cc_start: 0.8620 (t80) cc_final: 0.8180 (t80) REVERT: E 1666 ILE cc_start: 0.9039 (pp) cc_final: 0.8810 (pp) REVERT: E 1669 MET cc_start: 0.8831 (tpt) cc_final: 0.8628 (tpt) REVERT: E 1691 PHE cc_start: 0.9197 (t80) cc_final: 0.8900 (t80) REVERT: E 1696 LEU cc_start: 0.9458 (pp) cc_final: 0.9253 (pp) REVERT: E 1711 MET cc_start: 0.7606 (ttm) cc_final: 0.7315 (ppp) REVERT: E 1720 GLN cc_start: 0.8087 (pm20) cc_final: 0.7853 (pm20) REVERT: E 1937 TYR cc_start: 0.9002 (m-80) cc_final: 0.8787 (m-80) REVERT: E 2110 ARG cc_start: 0.8469 (ttm110) cc_final: 0.7479 (tpt170) REVERT: E 2282 LYS cc_start: 0.9113 (tttm) cc_final: 0.8878 (mtpp) REVERT: E 2301 ASN cc_start: 0.8736 (m-40) cc_final: 0.8488 (m110) REVERT: E 2364 TRP cc_start: 0.8786 (t60) cc_final: 0.8195 (t60) outliers start: 52 outliers final: 3 residues processed: 1581 average time/residue: 0.6062 time to fit residues: 1543.5980 Evaluate side-chains 956 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 945 time to evaluate : 5.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1292 ASN Chi-restraints excluded: chain F residue 1512 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1292 ASN Chi-restraints excluded: chain E residue 1512 ILE Chi-restraints excluded: chain E residue 1564 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 8.9990 chunk 433 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 0.0270 chunk 292 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 448 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 519 optimal weight: 0.4980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 HIS F 364 ASN F 367 ASN F 372 GLN F 548 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 682 GLN F 847 ASN ** F 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN F1073 GLN F1161 ASN F1335 ASN F1462 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1543 ASN F1557 GLN F1574 ASN F1591 GLN F1596 ASN F1619 ASN ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1699 ASN F1712 HIS F1756 ASN ** F1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2356 ASN C 189 ASN C 347 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 347 ASN D 437 ASN D 494 ASN ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 HIS ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN E 367 ASN E 548 HIS ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 633 GLN ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 GLN ** E 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 868 GLN E 951 HIS E 975 GLN E1073 GLN E1161 ASN E1335 ASN E1462 ASN ** E1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1557 GLN E1574 ASN ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1596 ASN E1618 GLN E1619 ASN E1625 HIS ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1699 ASN E1756 ASN ** E1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2356 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47082 Z= 0.198 Angle : 0.817 14.568 63787 Z= 0.405 Chirality : 0.045 0.245 7342 Planarity : 0.005 0.060 8019 Dihedral : 8.211 179.704 6262 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.67 % Allowed : 15.98 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.10), residues: 5688 helix: -1.34 (0.08), residues: 3580 sheet: -1.96 (0.49), residues: 64 loop : -3.25 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 487 HIS 0.014 0.001 HIS E1891 PHE 0.035 0.002 PHE C 399 TYR 0.032 0.002 TYR F1786 ARG 0.011 0.001 ARG F 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1120 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6916 (mm) REVERT: F 90 MET cc_start: 0.7721 (mmt) cc_final: 0.7436 (mmm) REVERT: F 120 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8713 (pp) REVERT: F 154 MET cc_start: 0.8406 (ttp) cc_final: 0.8079 (tmm) REVERT: F 186 TYR cc_start: 0.9121 (t80) cc_final: 0.8783 (t80) REVERT: F 238 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8751 (mt-10) REVERT: F 392 GLN cc_start: 0.7222 (mt0) cc_final: 0.6889 (tp40) REVERT: F 395 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9310 (tptp) REVERT: F 416 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8388 (mmm160) REVERT: F 487 TRP cc_start: 0.5225 (t60) cc_final: 0.4962 (t60) REVERT: F 545 PHE cc_start: 0.8689 (m-80) cc_final: 0.8473 (m-10) REVERT: F 579 ASN cc_start: 0.8088 (t0) cc_final: 0.7808 (t0) REVERT: F 629 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9024 (mp) REVERT: F 671 ASN cc_start: 0.8742 (m110) cc_final: 0.8363 (m110) REVERT: F 697 LYS cc_start: 0.9331 (mmtm) cc_final: 0.9046 (mmtt) REVERT: F 767 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7538 (p0) REVERT: F 947 PHE cc_start: 0.8700 (m-80) cc_final: 0.8422 (m-10) REVERT: F 1006 LEU cc_start: 0.8997 (tt) cc_final: 0.8779 (mt) REVERT: F 1060 GLN cc_start: 0.8738 (tp40) cc_final: 0.8070 (tp40) REVERT: F 1106 ARG cc_start: 0.9108 (ptp-110) cc_final: 0.8649 (mmm160) REVERT: F 1107 ASN cc_start: 0.8831 (m-40) cc_final: 0.7999 (t0) REVERT: F 1118 LYS cc_start: 0.9314 (ptpt) cc_final: 0.8963 (ptpt) REVERT: F 1126 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6866 (tm) REVERT: F 1245 TYR cc_start: 0.9069 (m-80) cc_final: 0.8799 (m-80) REVERT: F 1314 ASP cc_start: 0.9398 (t0) cc_final: 0.9064 (m-30) REVERT: F 1353 PHE cc_start: 0.8974 (m-10) cc_final: 0.8772 (m-80) REVERT: F 1447 ASP cc_start: 0.7702 (m-30) cc_final: 0.7328 (t70) REVERT: F 1451 LEU cc_start: 0.9026 (tp) cc_final: 0.8673 (mm) REVERT: F 1488 LYS cc_start: 0.8737 (pptt) cc_final: 0.8494 (pptt) REVERT: F 1503 MET cc_start: 0.8921 (ttp) cc_final: 0.8292 (tpp) REVERT: F 1510 SER cc_start: 0.9387 (m) cc_final: 0.9154 (p) REVERT: F 1536 SER cc_start: 0.8823 (t) cc_final: 0.8570 (t) REVERT: F 1651 TYR cc_start: 0.8572 (t80) cc_final: 0.8311 (t80) REVERT: F 1704 ASP cc_start: 0.8989 (p0) cc_final: 0.8735 (p0) REVERT: F 1720 GLN cc_start: 0.8012 (pm20) cc_final: 0.7520 (mp10) REVERT: F 1837 PHE cc_start: 0.8586 (m-10) cc_final: 0.8328 (m-80) REVERT: F 1897 TRP cc_start: 0.7071 (m100) cc_final: 0.6588 (m100) REVERT: F 2210 TYR cc_start: 0.8830 (t80) cc_final: 0.8443 (t80) REVERT: F 2225 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5798 (mmm-85) REVERT: F 2247 LEU cc_start: 0.8591 (mt) cc_final: 0.8302 (mp) REVERT: F 2263 ARG cc_start: 0.5499 (tmt-80) cc_final: 0.4439 (tpm170) REVERT: F 2282 LYS cc_start: 0.9167 (tttm) cc_final: 0.8802 (mtpp) REVERT: F 2292 MET cc_start: 0.8882 (ptp) cc_final: 0.8204 (ptp) REVERT: F 2295 ASN cc_start: 0.9273 (p0) cc_final: 0.8934 (t0) REVERT: F 2304 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8037 (tm-30) REVERT: F 2344 THR cc_start: 0.8585 (m) cc_final: 0.8112 (p) REVERT: F 2364 TRP cc_start: 0.8349 (t60) cc_final: 0.7909 (t60) REVERT: C 190 MET cc_start: 0.7407 (mpp) cc_final: 0.7175 (mmm) REVERT: C 201 ASP cc_start: 0.8195 (t0) cc_final: 0.7904 (m-30) REVERT: C 270 PHE cc_start: 0.8904 (t80) cc_final: 0.8703 (t80) REVERT: C 278 ILE cc_start: 0.9602 (mt) cc_final: 0.9240 (tp) REVERT: C 328 ASP cc_start: 0.8801 (p0) cc_final: 0.8398 (m-30) REVERT: C 373 GLU cc_start: 0.8315 (tt0) cc_final: 0.7870 (tt0) REVERT: C 437 ASN cc_start: 0.8218 (t0) cc_final: 0.7991 (p0) REVERT: C 540 LYS cc_start: 0.9429 (ptpp) cc_final: 0.9187 (ptpp) REVERT: C 547 LYS cc_start: 0.9061 (mttt) cc_final: 0.8792 (mttm) REVERT: C 562 ILE cc_start: 0.8046 (mt) cc_final: 0.7739 (mt) REVERT: C 575 LEU cc_start: 0.9229 (mt) cc_final: 0.8973 (mp) REVERT: C 588 LEU cc_start: 0.8232 (mp) cc_final: 0.7929 (mt) REVERT: C 610 HIS cc_start: 0.8868 (t-90) cc_final: 0.8340 (t-90) REVERT: C 654 THR cc_start: 0.6004 (p) cc_final: 0.5486 (p) REVERT: C 660 MET cc_start: 0.8969 (mtp) cc_final: 0.8583 (mmm) REVERT: C 664 ARG cc_start: 0.8956 (ptt180) cc_final: 0.8622 (ppt170) REVERT: D 208 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9017 (mm-30) REVERT: D 269 ARG cc_start: 0.9120 (mtp180) cc_final: 0.8868 (mtp85) REVERT: D 278 ILE cc_start: 0.9559 (mt) cc_final: 0.9189 (tp) REVERT: D 320 LYS cc_start: 0.9347 (tttt) cc_final: 0.9118 (tttt) REVERT: D 328 ASP cc_start: 0.8783 (p0) cc_final: 0.8355 (m-30) REVERT: D 373 GLU cc_start: 0.8360 (tt0) cc_final: 0.7788 (tt0) REVERT: D 403 TYR cc_start: 0.7613 (t80) cc_final: 0.7403 (t80) REVERT: D 547 LYS cc_start: 0.8976 (mttt) cc_final: 0.8631 (mttm) REVERT: D 593 TYR cc_start: 0.7798 (m-80) cc_final: 0.7251 (m-80) REVERT: D 609 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8462 (tp30) REVERT: D 610 HIS cc_start: 0.8876 (t-170) cc_final: 0.8529 (t-90) REVERT: D 612 LEU cc_start: 0.9233 (tp) cc_final: 0.8908 (tt) REVERT: D 661 ARG cc_start: 0.8998 (ptp-170) cc_final: 0.8716 (ptp90) REVERT: D 664 ARG cc_start: 0.9027 (ptt180) cc_final: 0.8572 (ppt170) REVERT: D 702 ASN cc_start: 0.9159 (m110) cc_final: 0.8734 (p0) REVERT: D 707 ARG cc_start: 0.8712 (mmt90) cc_final: 0.8398 (mmt-90) REVERT: D 720 MET cc_start: 0.7900 (mtm) cc_final: 0.7382 (ptm) REVERT: E 120 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8537 (pp) REVERT: E 126 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7581 (tppt) REVERT: E 154 MET cc_start: 0.8337 (ttp) cc_final: 0.8091 (tmm) REVERT: E 166 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8733 (pp) REVERT: E 186 TYR cc_start: 0.9114 (t80) cc_final: 0.8428 (t80) REVERT: E 238 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8717 (mt-10) REVERT: E 295 MET cc_start: 0.9034 (tpt) cc_final: 0.8569 (ptm) REVERT: E 318 HIS cc_start: 0.8510 (m-70) cc_final: 0.7655 (m90) REVERT: E 395 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9167 (tptp) REVERT: E 458 TRP cc_start: 0.8358 (m100) cc_final: 0.7693 (m100) REVERT: E 469 GLU cc_start: 0.8527 (tp30) cc_final: 0.8240 (tp30) REVERT: E 487 TRP cc_start: 0.4824 (t60) cc_final: 0.4550 (t60) REVERT: E 545 PHE cc_start: 0.9085 (m-80) cc_final: 0.8810 (m-80) REVERT: E 549 ARG cc_start: 0.9239 (mtt-85) cc_final: 0.8371 (tpp80) REVERT: E 587 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8621 (mt) REVERT: E 697 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8717 (mmtt) REVERT: E 811 LYS cc_start: 0.8889 (tmtm) cc_final: 0.8683 (tptt) REVERT: E 881 LEU cc_start: 0.8555 (pp) cc_final: 0.8343 (pp) REVERT: E 943 ARG cc_start: 0.8622 (mmt90) cc_final: 0.8396 (mpt-90) REVERT: E 947 PHE cc_start: 0.8936 (m-80) cc_final: 0.8596 (m-80) REVERT: E 951 HIS cc_start: 0.8326 (t-90) cc_final: 0.8069 (t-90) REVERT: E 1106 ARG cc_start: 0.9225 (ptp-110) cc_final: 0.8677 (mmm160) REVERT: E 1107 ASN cc_start: 0.8791 (m-40) cc_final: 0.8067 (t0) REVERT: E 1126 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6668 (tm) REVERT: E 1178 LEU cc_start: 0.8550 (mm) cc_final: 0.8274 (mm) REVERT: E 1245 TYR cc_start: 0.9009 (m-80) cc_final: 0.8723 (m-80) REVERT: E 1314 ASP cc_start: 0.9320 (t0) cc_final: 0.8975 (m-30) REVERT: E 1353 PHE cc_start: 0.8854 (m-80) cc_final: 0.8566 (m-80) REVERT: E 1451 LEU cc_start: 0.9067 (tp) cc_final: 0.8774 (mm) REVERT: E 1476 TRP cc_start: 0.8492 (p90) cc_final: 0.7475 (p90) REVERT: E 1503 MET cc_start: 0.8904 (ttp) cc_final: 0.8674 (ttp) REVERT: E 1510 SER cc_start: 0.9331 (m) cc_final: 0.9108 (p) REVERT: E 1536 SER cc_start: 0.8615 (t) cc_final: 0.8342 (t) REVERT: E 1666 ILE cc_start: 0.8980 (pp) cc_final: 0.8775 (pp) REVERT: E 1691 PHE cc_start: 0.9133 (t80) cc_final: 0.8894 (t80) REVERT: E 1711 MET cc_start: 0.7622 (ttm) cc_final: 0.7259 (ppp) REVERT: E 1720 GLN cc_start: 0.7990 (pm20) cc_final: 0.7653 (mp10) REVERT: E 1845 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.7751 (mtt90) REVERT: E 1897 TRP cc_start: 0.7156 (m100) cc_final: 0.6589 (m100) REVERT: E 2040 PHE cc_start: 0.6567 (m-80) cc_final: 0.6360 (m-80) REVERT: E 2065 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7934 (tp) REVERT: E 2247 LEU cc_start: 0.8714 (mt) cc_final: 0.8094 (mp) REVERT: E 2263 ARG cc_start: 0.5219 (tmt-80) cc_final: 0.4298 (tpm170) REVERT: E 2282 LYS cc_start: 0.9202 (tttm) cc_final: 0.8816 (mtpp) REVERT: E 2304 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 2344 THR cc_start: 0.8442 (m) cc_final: 0.8179 (p) REVERT: E 2349 GLN cc_start: 0.8921 (mp10) cc_final: 0.8695 (mp10) REVERT: E 2350 GLU cc_start: 0.8950 (tt0) cc_final: 0.8564 (pt0) REVERT: E 2364 TRP cc_start: 0.8742 (t60) cc_final: 0.7754 (t60) outliers start: 184 outliers final: 73 residues processed: 1225 average time/residue: 0.5878 time to fit residues: 1181.7615 Evaluate side-chains 989 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 903 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 841 LEU Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1455 LEU Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1771 LEU Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2084 VAL Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2225 ARG Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1632 PHE Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 432 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 520 optimal weight: 0.9990 chunk 562 optimal weight: 6.9990 chunk 463 optimal weight: 3.9990 chunk 516 optimal weight: 0.0270 chunk 177 optimal weight: 10.0000 chunk 417 optimal weight: 9.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 847 ASN ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1431 ASN F1507 GLN F1591 GLN ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN ** F2343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN D 213 HIS D 305 GLN D 334 HIS ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN E 548 HIS ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 868 GLN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1073 GLN ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1471 GLN ** E1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1955 HIS ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2192 ASN E2343 GLN E2356 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 47082 Z= 0.210 Angle : 0.796 13.507 63787 Z= 0.391 Chirality : 0.046 0.332 7342 Planarity : 0.005 0.055 8019 Dihedral : 7.651 179.423 6248 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.12 % Favored : 90.85 % Rotamer: Outliers : 4.57 % Allowed : 18.17 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.10), residues: 5688 helix: -0.86 (0.08), residues: 3592 sheet: -1.95 (0.47), residues: 66 loop : -3.10 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F1169 HIS 0.008 0.001 HIS F 951 PHE 0.035 0.002 PHE D 323 TYR 0.025 0.002 TYR E1786 ARG 0.009 0.001 ARG E2139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 956 time to evaluate : 4.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 90 MET cc_start: 0.7802 (mmt) cc_final: 0.7507 (mmm) REVERT: F 120 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (pp) REVERT: F 123 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8884 (ttm) REVERT: F 154 MET cc_start: 0.8270 (ttp) cc_final: 0.8036 (tmm) REVERT: F 186 TYR cc_start: 0.9089 (t80) cc_final: 0.8685 (t80) REVERT: F 191 GLU cc_start: 0.8384 (mp0) cc_final: 0.8137 (tp30) REVERT: F 211 PHE cc_start: 0.8054 (t80) cc_final: 0.7686 (t80) REVERT: F 297 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8152 (ttmm) REVERT: F 492 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8848 (tt) REVERT: F 576 CYS cc_start: 0.9007 (m) cc_final: 0.8712 (m) REVERT: F 587 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8552 (mt) REVERT: F 671 ASN cc_start: 0.8803 (m110) cc_final: 0.8386 (m110) REVERT: F 697 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8994 (mmtm) REVERT: F 759 MET cc_start: 0.9082 (tpp) cc_final: 0.8733 (tpp) REVERT: F 767 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7643 (p0) REVERT: F 816 ILE cc_start: 0.8476 (tp) cc_final: 0.8227 (tt) REVERT: F 928 GLN cc_start: 0.8689 (pm20) cc_final: 0.8385 (pp30) REVERT: F 947 PHE cc_start: 0.8872 (m-80) cc_final: 0.8591 (m-10) REVERT: F 1060 GLN cc_start: 0.8773 (tp40) cc_final: 0.8086 (tp40) REVERT: F 1106 ARG cc_start: 0.9106 (ptp-110) cc_final: 0.8641 (mmm160) REVERT: F 1107 ASN cc_start: 0.8808 (m-40) cc_final: 0.8029 (t0) REVERT: F 1118 LYS cc_start: 0.9342 (ptpt) cc_final: 0.8927 (ptpt) REVERT: F 1122 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8322 (mtm) REVERT: F 1126 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6758 (tm) REVERT: F 1245 TYR cc_start: 0.9069 (m-80) cc_final: 0.8766 (m-80) REVERT: F 1314 ASP cc_start: 0.9377 (t0) cc_final: 0.9081 (m-30) REVERT: F 1334 MET cc_start: 0.5041 (ptt) cc_final: 0.4805 (ptt) REVERT: F 1447 ASP cc_start: 0.7839 (m-30) cc_final: 0.7376 (t0) REVERT: F 1451 LEU cc_start: 0.9018 (tp) cc_final: 0.8664 (mm) REVERT: F 1488 LYS cc_start: 0.8748 (pptt) cc_final: 0.8473 (pptt) REVERT: F 1527 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7258 (mp) REVERT: F 1536 SER cc_start: 0.8784 (t) cc_final: 0.8507 (t) REVERT: F 1651 TYR cc_start: 0.8506 (t80) cc_final: 0.8293 (t80) REVERT: F 1837 PHE cc_start: 0.8443 (m-10) cc_final: 0.8205 (m-10) REVERT: F 1848 LEU cc_start: 0.9101 (mt) cc_final: 0.8749 (mp) REVERT: F 1897 TRP cc_start: 0.7198 (m100) cc_final: 0.6739 (m100) REVERT: F 2040 PHE cc_start: 0.6447 (m-80) cc_final: 0.6127 (m-80) REVERT: F 2210 TYR cc_start: 0.8844 (t80) cc_final: 0.8552 (t80) REVERT: F 2225 ARG cc_start: 0.6681 (mmm-85) cc_final: 0.6235 (mmm-85) REVERT: F 2263 ARG cc_start: 0.5473 (tmt-80) cc_final: 0.4436 (tpm170) REVERT: F 2282 LYS cc_start: 0.9185 (tttm) cc_final: 0.8814 (mtpp) REVERT: F 2292 MET cc_start: 0.8889 (ptp) cc_final: 0.8629 (ptm) REVERT: F 2295 ASN cc_start: 0.9267 (p0) cc_final: 0.8972 (t0) REVERT: F 2344 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8186 (p) REVERT: F 2349 GLN cc_start: 0.8798 (mp10) cc_final: 0.8529 (mp10) REVERT: F 2364 TRP cc_start: 0.8655 (t60) cc_final: 0.8384 (t60) REVERT: C 201 ASP cc_start: 0.8953 (t0) cc_final: 0.8246 (m-30) REVERT: C 278 ILE cc_start: 0.9573 (mt) cc_final: 0.9161 (mm) REVERT: C 303 MET cc_start: 0.8888 (ttm) cc_final: 0.8517 (mtp) REVERT: C 328 ASP cc_start: 0.8823 (p0) cc_final: 0.8425 (m-30) REVERT: C 373 GLU cc_start: 0.8467 (tt0) cc_final: 0.7966 (tt0) REVERT: C 414 MET cc_start: 0.8583 (tmm) cc_final: 0.8262 (tmm) REVERT: C 437 ASN cc_start: 0.8229 (t0) cc_final: 0.7308 (p0) REVERT: C 547 LYS cc_start: 0.9025 (mttt) cc_final: 0.8723 (mttm) REVERT: C 575 LEU cc_start: 0.9229 (mt) cc_final: 0.8882 (mp) REVERT: C 609 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8743 (tp30) REVERT: C 654 THR cc_start: 0.5757 (p) cc_final: 0.5275 (p) REVERT: C 660 MET cc_start: 0.8943 (mtp) cc_final: 0.8603 (mmm) REVERT: C 664 ARG cc_start: 0.9064 (ptt180) cc_final: 0.8681 (ppt170) REVERT: D 190 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7473 (mmm) REVERT: D 278 ILE cc_start: 0.9553 (mt) cc_final: 0.9261 (tp) REVERT: D 328 ASP cc_start: 0.8801 (p0) cc_final: 0.8352 (m-30) REVERT: D 547 LYS cc_start: 0.8968 (mttt) cc_final: 0.8650 (mttm) REVERT: D 561 MET cc_start: 0.7919 (mmm) cc_final: 0.7266 (mmm) REVERT: D 593 TYR cc_start: 0.7875 (m-80) cc_final: 0.7241 (m-80) REVERT: D 609 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8421 (tp30) REVERT: D 610 HIS cc_start: 0.8885 (t-170) cc_final: 0.8544 (t-90) REVERT: D 661 ARG cc_start: 0.8920 (ptp-170) cc_final: 0.8671 (ptp90) REVERT: D 664 ARG cc_start: 0.9014 (ptt180) cc_final: 0.8579 (ppt170) REVERT: D 702 ASN cc_start: 0.9142 (m110) cc_final: 0.8758 (p0) REVERT: D 720 MET cc_start: 0.7892 (mtm) cc_final: 0.7396 (ptm) REVERT: E 120 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8124 (pp) REVERT: E 126 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7573 (tppt) REVERT: E 154 MET cc_start: 0.8407 (ttp) cc_final: 0.8197 (tmm) REVERT: E 186 TYR cc_start: 0.9081 (t80) cc_final: 0.8334 (t80) REVERT: E 208 PHE cc_start: 0.6756 (t80) cc_final: 0.5586 (t80) REVERT: E 238 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8847 (mt-10) REVERT: E 295 MET cc_start: 0.8947 (tpt) cc_final: 0.8580 (ptm) REVERT: E 297 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7537 (ttmm) REVERT: E 318 HIS cc_start: 0.8725 (m-70) cc_final: 0.7715 (m90) REVERT: E 395 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9148 (tptp) REVERT: E 469 GLU cc_start: 0.8607 (tp30) cc_final: 0.8314 (tp30) REVERT: E 484 MET cc_start: 0.7072 (ptt) cc_final: 0.6589 (ptt) REVERT: E 539 LEU cc_start: 0.9308 (tp) cc_final: 0.9055 (mt) REVERT: E 545 PHE cc_start: 0.9170 (m-80) cc_final: 0.8813 (m-80) REVERT: E 549 ARG cc_start: 0.9303 (mtt-85) cc_final: 0.8306 (tpp80) REVERT: E 551 PHE cc_start: 0.9021 (m-10) cc_final: 0.8369 (m-80) REVERT: E 590 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.7832 (mtp-110) REVERT: E 605 ASP cc_start: 0.8943 (m-30) cc_final: 0.8502 (t0) REVERT: E 631 TRP cc_start: 0.9051 (m100) cc_final: 0.8384 (m100) REVERT: E 668 GLN cc_start: 0.9251 (mm110) cc_final: 0.8949 (mm-40) REVERT: E 697 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8765 (mmtt) REVERT: E 747 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8587 (tp) REVERT: E 902 GLU cc_start: 0.8779 (mp0) cc_final: 0.7800 (pt0) REVERT: E 945 GLU cc_start: 0.8991 (pt0) cc_final: 0.8762 (pt0) REVERT: E 947 PHE cc_start: 0.8996 (m-80) cc_final: 0.8562 (m-80) REVERT: E 1106 ARG cc_start: 0.9186 (ptp-110) cc_final: 0.8693 (mmm160) REVERT: E 1126 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6574 (tm) REVERT: E 1178 LEU cc_start: 0.8577 (mm) cc_final: 0.8302 (mm) REVERT: E 1245 TYR cc_start: 0.9034 (m-80) cc_final: 0.8745 (m-80) REVERT: E 1314 ASP cc_start: 0.9261 (t0) cc_final: 0.8970 (m-30) REVERT: E 1353 PHE cc_start: 0.8907 (m-10) cc_final: 0.8674 (m-80) REVERT: E 1476 TRP cc_start: 0.8484 (p90) cc_final: 0.7749 (p90) REVERT: E 1527 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7511 (mp) REVERT: E 1536 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8292 (t) REVERT: E 1574 ASN cc_start: 0.8441 (m110) cc_final: 0.8204 (m110) REVERT: E 1691 PHE cc_start: 0.9169 (t80) cc_final: 0.8950 (t80) REVERT: E 1720 GLN cc_start: 0.7908 (pm20) cc_final: 0.7613 (mp10) REVERT: E 1874 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7977 (pp) REVERT: E 1897 TRP cc_start: 0.7277 (m100) cc_final: 0.6764 (m100) REVERT: E 2040 PHE cc_start: 0.6672 (m-80) cc_final: 0.6412 (m-80) REVERT: E 2247 LEU cc_start: 0.8793 (mt) cc_final: 0.8351 (mp) REVERT: E 2282 LYS cc_start: 0.9170 (tttm) cc_final: 0.8815 (mtpp) REVERT: E 2292 MET cc_start: 0.8819 (ptp) cc_final: 0.8056 (ptp) REVERT: E 2304 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8071 (tm-30) REVERT: E 2350 GLU cc_start: 0.8931 (tt0) cc_final: 0.8556 (pt0) outliers start: 230 outliers final: 122 residues processed: 1107 average time/residue: 0.5498 time to fit residues: 1011.7448 Evaluate side-chains 990 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 851 time to evaluate : 5.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1122 MET Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1500 LEU Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1771 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2084 VAL Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2343 GLN Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain F residue 2355 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1354 GLU Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1874 LEU Chi-restraints excluded: chain E residue 1906 SER Chi-restraints excluded: chain E residue 1955 HIS Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2110 ARG Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 0.9990 chunk 391 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 349 optimal weight: 6.9990 chunk 522 optimal weight: 0.6980 chunk 552 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 494 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN F2241 HIS ** F2343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 GLN ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 GLN ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1743 GLN ** E1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1955 HIS ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2192 ASN E2241 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 47082 Z= 0.193 Angle : 0.789 15.306 63787 Z= 0.383 Chirality : 0.045 0.333 7342 Planarity : 0.004 0.052 8019 Dihedral : 7.338 179.962 6248 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.41 % Allowed : 19.33 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.11), residues: 5688 helix: -0.66 (0.08), residues: 3576 sheet: -2.21 (0.45), residues: 80 loop : -2.95 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F1169 HIS 0.013 0.001 HIS F1955 PHE 0.030 0.002 PHE F1353 TYR 0.025 0.001 TYR E1786 ARG 0.009 0.001 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 941 time to evaluate : 5.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 63 ILE cc_start: 0.8124 (mm) cc_final: 0.7769 (mm) REVERT: F 90 MET cc_start: 0.7758 (mmt) cc_final: 0.7518 (mmm) REVERT: F 120 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8702 (tp) REVERT: F 140 LYS cc_start: 0.7992 (tptt) cc_final: 0.7722 (mmtp) REVERT: F 186 TYR cc_start: 0.9096 (t80) cc_final: 0.8639 (t80) REVERT: F 211 PHE cc_start: 0.8045 (t80) cc_final: 0.7781 (t80) REVERT: F 295 MET cc_start: 0.9097 (tpt) cc_final: 0.7988 (ptm) REVERT: F 395 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9317 (tptp) REVERT: F 430 ASN cc_start: 0.6605 (m-40) cc_final: 0.6332 (m-40) REVERT: F 484 MET cc_start: 0.8447 (mtt) cc_final: 0.7858 (ptp) REVERT: F 570 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8333 (t80) REVERT: F 587 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8760 (mt) REVERT: F 718 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8655 (mmmt) REVERT: F 759 MET cc_start: 0.9126 (tpp) cc_final: 0.8909 (tmm) REVERT: F 816 ILE cc_start: 0.8427 (tp) cc_final: 0.8165 (tt) REVERT: F 928 GLN cc_start: 0.8628 (pm20) cc_final: 0.8372 (pp30) REVERT: F 947 PHE cc_start: 0.8927 (m-80) cc_final: 0.8322 (m-10) REVERT: F 1060 GLN cc_start: 0.8783 (tp40) cc_final: 0.8086 (tp40) REVERT: F 1099 LEU cc_start: 0.9400 (mt) cc_final: 0.9121 (pp) REVERT: F 1106 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8542 (mmt180) REVERT: F 1107 ASN cc_start: 0.8875 (m-40) cc_final: 0.8170 (t0) REVERT: F 1109 ASP cc_start: 0.7660 (t0) cc_final: 0.7407 (p0) REVERT: F 1118 LYS cc_start: 0.9288 (ptpt) cc_final: 0.8885 (ptpt) REVERT: F 1126 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6664 (tm) REVERT: F 1155 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: F 1245 TYR cc_start: 0.9049 (m-80) cc_final: 0.8721 (m-80) REVERT: F 1314 ASP cc_start: 0.9392 (t0) cc_final: 0.9104 (m-30) REVERT: F 1334 MET cc_start: 0.4974 (ptt) cc_final: 0.4676 (ptt) REVERT: F 1353 PHE cc_start: 0.9009 (m-80) cc_final: 0.8662 (m-80) REVERT: F 1447 ASP cc_start: 0.7722 (m-30) cc_final: 0.7418 (t70) REVERT: F 1451 LEU cc_start: 0.9051 (tp) cc_final: 0.8753 (mm) REVERT: F 1485 VAL cc_start: 0.9444 (p) cc_final: 0.9190 (m) REVERT: F 1488 LYS cc_start: 0.8705 (pptt) cc_final: 0.8440 (pptt) REVERT: F 1503 MET cc_start: 0.8754 (ttm) cc_final: 0.8452 (ttp) REVERT: F 1527 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7193 (mp) REVERT: F 1536 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8444 (t) REVERT: F 1651 TYR cc_start: 0.8498 (t80) cc_final: 0.8289 (t80) REVERT: F 1724 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: F 1897 TRP cc_start: 0.7321 (m100) cc_final: 0.6817 (m100) REVERT: F 1920 MET cc_start: 0.9159 (mmm) cc_final: 0.8610 (tmm) REVERT: F 2008 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6542 (mmm) REVERT: F 2020 ARG cc_start: 0.8758 (ptt180) cc_final: 0.8443 (ttp-170) REVERT: F 2040 PHE cc_start: 0.6419 (m-80) cc_final: 0.6104 (m-80) REVERT: F 2227 CYS cc_start: 0.8409 (m) cc_final: 0.8150 (m) REVERT: F 2247 LEU cc_start: 0.8933 (mt) cc_final: 0.7991 (pt) REVERT: F 2263 ARG cc_start: 0.5258 (tmt-80) cc_final: 0.4866 (tpm170) REVERT: F 2282 LYS cc_start: 0.9273 (tttm) cc_final: 0.8872 (mtpp) REVERT: F 2304 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8093 (tm-30) REVERT: F 2344 THR cc_start: 0.8425 (m) cc_final: 0.8016 (t) REVERT: F 2364 TRP cc_start: 0.8894 (t60) cc_final: 0.8451 (t60) REVERT: C 190 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7271 (mmp) REVERT: C 201 ASP cc_start: 0.8978 (t0) cc_final: 0.8355 (m-30) REVERT: C 303 MET cc_start: 0.8836 (ttm) cc_final: 0.8629 (mmm) REVERT: C 328 ASP cc_start: 0.8751 (p0) cc_final: 0.8398 (m-30) REVERT: C 373 GLU cc_start: 0.8412 (tt0) cc_final: 0.8157 (tt0) REVERT: C 377 ARG cc_start: 0.8982 (mtp-110) cc_final: 0.7690 (ttp80) REVERT: C 400 GLU cc_start: 0.9344 (tt0) cc_final: 0.8917 (tt0) REVERT: C 414 MET cc_start: 0.8732 (tmm) cc_final: 0.8431 (tmm) REVERT: C 437 ASN cc_start: 0.7897 (t0) cc_final: 0.7588 (p0) REVERT: C 449 TRP cc_start: 0.7609 (t60) cc_final: 0.6950 (t60) REVERT: C 575 LEU cc_start: 0.9260 (mt) cc_final: 0.8871 (mp) REVERT: C 591 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 609 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8680 (tp30) REVERT: C 664 ARG cc_start: 0.9048 (ptt180) cc_final: 0.8663 (ppt170) REVERT: D 190 MET cc_start: 0.8114 (mmm) cc_final: 0.7526 (mmm) REVERT: D 328 ASP cc_start: 0.8730 (p0) cc_final: 0.8315 (m-30) REVERT: D 400 GLU cc_start: 0.9297 (tt0) cc_final: 0.8809 (tt0) REVERT: D 449 TRP cc_start: 0.7622 (t60) cc_final: 0.6939 (t60) REVERT: D 547 LYS cc_start: 0.8943 (mttt) cc_final: 0.8630 (mttm) REVERT: D 593 TYR cc_start: 0.7781 (m-80) cc_final: 0.7232 (m-80) REVERT: D 609 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8333 (tp30) REVERT: D 610 HIS cc_start: 0.8970 (t-170) cc_final: 0.8662 (t-90) REVERT: D 661 ARG cc_start: 0.8873 (ptp-170) cc_final: 0.8210 (ptp90) REVERT: D 664 ARG cc_start: 0.9027 (ptt180) cc_final: 0.8512 (ppt170) REVERT: D 702 ASN cc_start: 0.9105 (m110) cc_final: 0.8779 (p0) REVERT: D 720 MET cc_start: 0.7869 (mtm) cc_final: 0.7431 (ptm) REVERT: E 120 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8604 (pp) REVERT: E 154 MET cc_start: 0.8373 (ttp) cc_final: 0.8153 (tmm) REVERT: E 186 TYR cc_start: 0.9053 (t80) cc_final: 0.8262 (t80) REVERT: E 208 PHE cc_start: 0.7038 (t80) cc_final: 0.5797 (t80) REVERT: E 295 MET cc_start: 0.8892 (tpt) cc_final: 0.8566 (ptm) REVERT: E 297 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7737 (ttpp) REVERT: E 395 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9053 (tptp) REVERT: E 469 GLU cc_start: 0.8645 (tp30) cc_final: 0.8346 (tp30) REVERT: E 539 LEU cc_start: 0.9307 (tp) cc_final: 0.9010 (mt) REVERT: E 545 PHE cc_start: 0.9186 (m-80) cc_final: 0.8833 (m-80) REVERT: E 549 ARG cc_start: 0.9189 (mtt-85) cc_final: 0.8181 (tpp80) REVERT: E 551 PHE cc_start: 0.8985 (m-10) cc_final: 0.8290 (m-80) REVERT: E 605 ASP cc_start: 0.8944 (m-30) cc_final: 0.8525 (t0) REVERT: E 631 TRP cc_start: 0.8974 (m100) cc_final: 0.8493 (m100) REVERT: E 668 GLN cc_start: 0.9187 (mm110) cc_final: 0.8944 (mm110) REVERT: E 697 LYS cc_start: 0.9303 (mmtm) cc_final: 0.8999 (mmtt) REVERT: E 718 LYS cc_start: 0.8939 (tttt) cc_final: 0.8708 (mmmt) REVERT: E 748 MET cc_start: 0.8955 (mmm) cc_final: 0.8638 (mmm) REVERT: E 943 ARG cc_start: 0.8508 (mmt90) cc_final: 0.8243 (mmm-85) REVERT: E 947 PHE cc_start: 0.8993 (m-80) cc_final: 0.8402 (m-80) REVERT: E 1106 ARG cc_start: 0.9157 (ptp-110) cc_final: 0.8606 (mmt180) REVERT: E 1126 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6375 (tm) REVERT: E 1134 LYS cc_start: 0.8148 (tttp) cc_final: 0.7873 (tptt) REVERT: E 1178 LEU cc_start: 0.8679 (mm) cc_final: 0.8394 (mm) REVERT: E 1353 PHE cc_start: 0.9015 (m-10) cc_final: 0.8651 (m-80) REVERT: E 1503 MET cc_start: 0.8928 (ttm) cc_final: 0.8526 (ttp) REVERT: E 1536 SER cc_start: 0.8559 (t) cc_final: 0.8273 (t) REVERT: E 1574 ASN cc_start: 0.8611 (m110) cc_final: 0.8300 (m110) REVERT: E 1666 ILE cc_start: 0.9120 (pp) cc_final: 0.8920 (pp) REVERT: E 1704 ASP cc_start: 0.9146 (p0) cc_final: 0.8865 (p0) REVERT: E 1711 MET cc_start: 0.7694 (ttm) cc_final: 0.7433 (ttm) REVERT: E 1720 GLN cc_start: 0.8015 (pm20) cc_final: 0.7447 (mp10) REVERT: E 1897 TRP cc_start: 0.7429 (m100) cc_final: 0.6897 (m100) REVERT: E 2040 PHE cc_start: 0.6678 (m-80) cc_final: 0.6428 (m-80) REVERT: E 2092 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8587 (tp-100) REVERT: E 2210 TYR cc_start: 0.8518 (t80) cc_final: 0.8051 (t80) REVERT: E 2263 ARG cc_start: 0.5060 (tpm170) cc_final: 0.4277 (tpm170) REVERT: E 2282 LYS cc_start: 0.9268 (tttm) cc_final: 0.8906 (mtpp) REVERT: E 2304 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8178 (tm-30) REVERT: E 2349 GLN cc_start: 0.8902 (mp10) cc_final: 0.8699 (mp10) REVERT: E 2350 GLU cc_start: 0.8922 (tt0) cc_final: 0.8558 (pt0) outliers start: 221 outliers final: 118 residues processed: 1093 average time/residue: 0.5608 time to fit residues: 1024.0224 Evaluate side-chains 972 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 839 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 699 LEU Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1536 SER Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1771 LEU Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1906 SER Chi-restraints excluded: chain F residue 2008 MET Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2119 VAL Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2355 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1165 VAL Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1510 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1906 SER Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2116 ILE Chi-restraints excluded: chain E residue 2119 VAL Chi-restraints excluded: chain E residue 2132 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 411 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 471 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 282 optimal weight: 5.9990 chunk 496 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 ASN F 426 GLN ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN F 671 ASN F 682 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 GLN ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1235 GLN ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1847 ASN ** F1945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN F2229 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS C 494 ASN C 554 ASN ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 HIS D 290 ASN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 HIS E 197 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 868 GLN ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1235 GLN ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1431 ASN E1471 GLN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1543 ASN E1574 ASN ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1595 HIS E1604 ASN ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2192 ASN E2229 ASN E2356 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 47082 Z= 0.310 Angle : 0.833 12.789 63787 Z= 0.419 Chirality : 0.047 0.387 7342 Planarity : 0.005 0.058 8019 Dihedral : 7.402 176.452 6248 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 29.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.27 % Allowed : 20.00 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.11), residues: 5688 helix: -0.66 (0.08), residues: 3614 sheet: -2.17 (0.46), residues: 78 loop : -2.96 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 487 HIS 0.026 0.002 HIS D 334 PHE 0.037 0.003 PHE C 323 TYR 0.030 0.002 TYR E2361 ARG 0.007 0.001 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 837 time to evaluate : 5.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 186 TYR cc_start: 0.9023 (t80) cc_final: 0.8799 (t80) REVERT: F 211 PHE cc_start: 0.8069 (t80) cc_final: 0.7865 (t80) REVERT: F 289 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.3666 (tt) REVERT: F 295 MET cc_start: 0.9206 (tpt) cc_final: 0.8160 (ptm) REVERT: F 297 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8080 (ttmm) REVERT: F 307 ILE cc_start: 0.9477 (pt) cc_final: 0.9043 (mm) REVERT: F 395 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9250 (tptp) REVERT: F 416 ARG cc_start: 0.9392 (mmm160) cc_final: 0.8844 (mmm160) REVERT: F 484 MET cc_start: 0.8505 (mtt) cc_final: 0.8170 (mtt) REVERT: F 539 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8991 (mt) REVERT: F 691 LEU cc_start: 0.8938 (tp) cc_final: 0.8490 (mt) REVERT: F 697 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8692 (mmtt) REVERT: F 728 ILE cc_start: 0.9189 (pt) cc_final: 0.8965 (tp) REVERT: F 759 MET cc_start: 0.9182 (tpp) cc_final: 0.8927 (tmm) REVERT: F 767 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8008 (p0) REVERT: F 947 PHE cc_start: 0.9155 (m-80) cc_final: 0.8947 (m-10) REVERT: F 1060 GLN cc_start: 0.8857 (tp40) cc_final: 0.8176 (tp40) REVERT: F 1106 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8184 (mmt-90) REVERT: F 1118 LYS cc_start: 0.9407 (ptpt) cc_final: 0.9094 (ptpp) REVERT: F 1126 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6820 (tm) REVERT: F 1134 LYS cc_start: 0.8436 (tttp) cc_final: 0.8098 (ptmt) REVERT: F 1245 TYR cc_start: 0.9126 (m-80) cc_final: 0.8793 (m-80) REVERT: F 1314 ASP cc_start: 0.9388 (t0) cc_final: 0.9110 (m-30) REVERT: F 1349 ILE cc_start: 0.8935 (mt) cc_final: 0.8734 (pt) REVERT: F 1353 PHE cc_start: 0.9164 (m-80) cc_final: 0.8788 (m-80) REVERT: F 1447 ASP cc_start: 0.7724 (m-30) cc_final: 0.7523 (t70) REVERT: F 1485 VAL cc_start: 0.9430 (p) cc_final: 0.9202 (m) REVERT: F 1488 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (pptt) REVERT: F 1503 MET cc_start: 0.8901 (ttm) cc_final: 0.8415 (ttp) REVERT: F 1527 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7233 (mp) REVERT: F 1574 ASN cc_start: 0.8728 (m110) cc_final: 0.8200 (m110) REVERT: F 1615 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (mt) REVERT: F 1711 MET cc_start: 0.8470 (ttm) cc_final: 0.8147 (ttm) REVERT: F 1724 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: F 1890 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: F 1897 TRP cc_start: 0.7584 (m100) cc_final: 0.7266 (m100) REVERT: F 1920 MET cc_start: 0.9154 (mmm) cc_final: 0.8639 (tmm) REVERT: F 2020 ARG cc_start: 0.8875 (ptt180) cc_final: 0.8586 (ttp-170) REVERT: F 2040 PHE cc_start: 0.6417 (m-80) cc_final: 0.6041 (m-80) REVERT: F 2263 ARG cc_start: 0.5351 (tmt-80) cc_final: 0.4931 (tpm170) REVERT: F 2282 LYS cc_start: 0.9256 (tttm) cc_final: 0.8876 (mtpt) REVERT: F 2296 GLU cc_start: 0.8989 (pm20) cc_final: 0.8778 (pp20) REVERT: F 2304 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 2364 TRP cc_start: 0.8998 (t60) cc_final: 0.8708 (t60) REVERT: C 190 MET cc_start: 0.7989 (mmm) cc_final: 0.7302 (mmp) REVERT: C 201 ASP cc_start: 0.9084 (t0) cc_final: 0.8495 (m-30) REVERT: C 303 MET cc_start: 0.8895 (ttm) cc_final: 0.8370 (mtp) REVERT: C 400 GLU cc_start: 0.9292 (tt0) cc_final: 0.8826 (tt0) REVERT: C 437 ASN cc_start: 0.8193 (t0) cc_final: 0.7925 (p0) REVERT: C 449 TRP cc_start: 0.7766 (t60) cc_final: 0.6917 (t60) REVERT: C 547 LYS cc_start: 0.9055 (mttt) cc_final: 0.8805 (mttm) REVERT: C 574 MET cc_start: 0.8364 (mmm) cc_final: 0.8042 (mmm) REVERT: C 609 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8832 (tm-30) REVERT: C 610 HIS cc_start: 0.9114 (t-170) cc_final: 0.8783 (t-90) REVERT: C 640 MET cc_start: 0.9208 (ttm) cc_final: 0.8879 (tmm) REVERT: C 664 ARG cc_start: 0.9125 (ptt180) cc_final: 0.8787 (ppt170) REVERT: D 238 LYS cc_start: 0.9010 (tttm) cc_final: 0.8776 (tptp) REVERT: D 449 TRP cc_start: 0.7836 (t60) cc_final: 0.7608 (t60) REVERT: D 547 LYS cc_start: 0.8927 (mttt) cc_final: 0.8676 (mttm) REVERT: D 593 TYR cc_start: 0.7976 (m-80) cc_final: 0.7323 (m-80) REVERT: D 609 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8657 (tp30) REVERT: D 610 HIS cc_start: 0.9115 (t-170) cc_final: 0.8792 (t-90) REVERT: D 612 LEU cc_start: 0.8987 (tp) cc_final: 0.8719 (mp) REVERT: D 664 ARG cc_start: 0.9183 (ptt180) cc_final: 0.8650 (ppt170) REVERT: D 720 MET cc_start: 0.7950 (mtm) cc_final: 0.7656 (ptm) REVERT: E 126 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7502 (tppt) REVERT: E 208 PHE cc_start: 0.7662 (t80) cc_final: 0.7251 (t80) REVERT: E 295 MET cc_start: 0.9030 (tpt) cc_final: 0.8651 (ptm) REVERT: E 347 TYR cc_start: 0.8963 (t80) cc_final: 0.8607 (t80) REVERT: E 416 ARG cc_start: 0.9164 (mmm160) cc_final: 0.8554 (mmm160) REVERT: E 539 LEU cc_start: 0.9360 (tp) cc_final: 0.9091 (mt) REVERT: E 549 ARG cc_start: 0.9168 (mtt-85) cc_final: 0.8510 (ttm170) REVERT: E 587 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8697 (mm) REVERT: E 664 MET cc_start: 0.8200 (ttm) cc_final: 0.7835 (ttm) REVERT: E 668 GLN cc_start: 0.9143 (mm110) cc_final: 0.8865 (mm110) REVERT: E 724 PHE cc_start: 0.9053 (m-80) cc_final: 0.8844 (m-80) REVERT: E 748 MET cc_start: 0.9013 (mmm) cc_final: 0.8751 (mmm) REVERT: E 947 PHE cc_start: 0.9231 (m-80) cc_final: 0.8765 (m-80) REVERT: E 1106 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8288 (mmt-90) REVERT: E 1126 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6923 (tm) REVERT: E 1134 LYS cc_start: 0.8126 (tttp) cc_final: 0.7851 (tptt) REVERT: E 1245 TYR cc_start: 0.9138 (m-80) cc_final: 0.8833 (m-80) REVERT: E 1314 ASP cc_start: 0.9276 (t0) cc_final: 0.8784 (m-30) REVERT: E 1350 PHE cc_start: 0.8452 (t80) cc_final: 0.8163 (t80) REVERT: E 1351 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8803 (ttp80) REVERT: E 1353 PHE cc_start: 0.9062 (m-10) cc_final: 0.8742 (m-80) REVERT: E 1574 ASN cc_start: 0.8859 (m-40) cc_final: 0.8534 (m110) REVERT: E 1615 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8615 (mt) REVERT: E 1622 MET cc_start: 0.8145 (tpt) cc_final: 0.7558 (tpt) REVERT: E 1666 ILE cc_start: 0.9165 (pp) cc_final: 0.8936 (pp) REVERT: E 1879 GLU cc_start: 0.9176 (tp30) cc_final: 0.8869 (pp20) REVERT: E 2040 PHE cc_start: 0.6815 (m-80) cc_final: 0.6523 (m-80) REVERT: E 2093 PHE cc_start: 0.9387 (t80) cc_final: 0.9052 (t80) REVERT: E 2263 ARG cc_start: 0.5181 (tpm170) cc_final: 0.4535 (tpm170) REVERT: E 2282 LYS cc_start: 0.9236 (tttm) cc_final: 0.8865 (mtpp) REVERT: E 2292 MET cc_start: 0.8815 (ptp) cc_final: 0.8219 (ptp) REVERT: E 2301 ASN cc_start: 0.8670 (m110) cc_final: 0.8352 (p0) REVERT: E 2304 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8290 (tm-30) REVERT: E 2350 GLU cc_start: 0.8686 (tt0) cc_final: 0.8388 (pt0) outliers start: 265 outliers final: 166 residues processed: 1019 average time/residue: 0.5462 time to fit residues: 937.5670 Evaluate side-chains 938 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 755 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 250 TYR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1390 GLU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1510 SER Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1615 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 1906 SER Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2164 HIS Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2312 MET Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 596 GLN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1390 GLU Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1510 SER Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1615 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1906 SER Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2110 ARG Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2176 GLU Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain E residue 2355 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 8.9990 chunk 497 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 324 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 553 optimal weight: 4.9990 chunk 459 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 183 optimal weight: 0.0970 chunk 290 optimal weight: 6.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN F 525 ASN ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN F 682 GLN ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 GLN ** F 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1618 GLN ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1785 GLN F1787 GLN ** F1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2089 GLN F2177 GLN F2192 ASN ** F2343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2356 ASN C 290 ASN C 334 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1439 GLN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1787 GLN E1847 ASN ** E1945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2356 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47082 Z= 0.215 Angle : 0.806 12.988 63787 Z= 0.394 Chirality : 0.046 0.338 7342 Planarity : 0.004 0.052 8019 Dihedral : 7.204 179.369 6244 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.31 % Allowed : 21.88 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 5688 helix: -0.50 (0.08), residues: 3598 sheet: -1.85 (0.47), residues: 80 loop : -2.86 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E1897 HIS 0.015 0.001 HIS F 149 PHE 0.063 0.002 PHE F1837 TYR 0.048 0.002 TYR F 175 ARG 0.008 0.001 ARG F 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 834 time to evaluate : 5.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 289 LEU cc_start: 0.4173 (OUTLIER) cc_final: 0.3574 (tt) REVERT: F 295 MET cc_start: 0.9107 (tpt) cc_final: 0.8175 (ptt) REVERT: F 307 ILE cc_start: 0.9464 (pt) cc_final: 0.9029 (mm) REVERT: F 416 ARG cc_start: 0.9441 (mmm160) cc_final: 0.8841 (mmm160) REVERT: F 484 MET cc_start: 0.8609 (mtt) cc_final: 0.8370 (mtt) REVERT: F 539 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8914 (mt) REVERT: F 671 ASN cc_start: 0.8853 (m-40) cc_final: 0.8381 (m110) REVERT: F 697 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8797 (mmtt) REVERT: F 718 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8376 (mmmm) REVERT: F 728 ILE cc_start: 0.9143 (pt) cc_final: 0.8889 (tp) REVERT: F 759 MET cc_start: 0.9144 (tpp) cc_final: 0.8890 (tmm) REVERT: F 767 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8134 (p0) REVERT: F 943 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8258 (mmt90) REVERT: F 947 PHE cc_start: 0.9041 (m-80) cc_final: 0.8658 (m-80) REVERT: F 983 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8151 (ptmt) REVERT: F 1020 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8144 (tt) REVERT: F 1060 GLN cc_start: 0.8848 (tp40) cc_final: 0.8170 (tp40) REVERT: F 1106 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8348 (mmt-90) REVERT: F 1118 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9046 (ptpp) REVERT: F 1126 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6628 (tm) REVERT: F 1245 TYR cc_start: 0.9106 (m-80) cc_final: 0.8889 (m-80) REVERT: F 1314 ASP cc_start: 0.9381 (t0) cc_final: 0.9117 (m-30) REVERT: F 1349 ILE cc_start: 0.8993 (mt) cc_final: 0.8774 (pt) REVERT: F 1353 PHE cc_start: 0.9217 (m-80) cc_final: 0.8860 (m-80) REVERT: F 1447 ASP cc_start: 0.7581 (m-30) cc_final: 0.7312 (t70) REVERT: F 1485 VAL cc_start: 0.9468 (p) cc_final: 0.9204 (m) REVERT: F 1488 LYS cc_start: 0.8686 (pptt) cc_final: 0.8450 (pptt) REVERT: F 1527 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7196 (mp) REVERT: F 1574 ASN cc_start: 0.8755 (m110) cc_final: 0.8260 (m110) REVERT: F 1615 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8560 (mt) REVERT: F 1731 LYS cc_start: 0.9158 (ptmt) cc_final: 0.8854 (mmtm) REVERT: F 1837 PHE cc_start: 0.8569 (m-80) cc_final: 0.8207 (m-80) REVERT: F 1890 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: F 1897 TRP cc_start: 0.7610 (m100) cc_final: 0.7291 (m100) REVERT: F 1920 MET cc_start: 0.9140 (mmm) cc_final: 0.8528 (tmm) REVERT: F 2008 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.6945 (mmm) REVERT: F 2020 ARG cc_start: 0.8892 (ptt180) cc_final: 0.8612 (ttp-170) REVERT: F 2065 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7569 (tp) REVERT: F 2097 MET cc_start: 0.9391 (mmm) cc_final: 0.9185 (tpt) REVERT: F 2110 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7883 (tpt170) REVERT: F 2213 MET cc_start: 0.8400 (mmm) cc_final: 0.8171 (mmm) REVERT: F 2247 LEU cc_start: 0.8956 (mt) cc_final: 0.8601 (mp) REVERT: F 2263 ARG cc_start: 0.5424 (tmt-80) cc_final: 0.4650 (tpm170) REVERT: F 2282 LYS cc_start: 0.9243 (tttm) cc_final: 0.8792 (mtpt) REVERT: F 2292 MET cc_start: 0.8867 (ptp) cc_final: 0.8344 (ptp) REVERT: F 2304 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8199 (tm-30) REVERT: F 2350 GLU cc_start: 0.8532 (pt0) cc_final: 0.8301 (pt0) REVERT: C 201 ASP cc_start: 0.9073 (t0) cc_final: 0.8560 (m-30) REVERT: C 260 ARG cc_start: 0.8222 (ptp-170) cc_final: 0.7888 (ptt180) REVERT: C 269 ARG cc_start: 0.8363 (tpm170) cc_final: 0.8006 (tpm170) REVERT: C 328 ASP cc_start: 0.8618 (p0) cc_final: 0.8337 (m-30) REVERT: C 400 GLU cc_start: 0.9320 (tt0) cc_final: 0.8777 (tt0) REVERT: C 437 ASN cc_start: 0.8186 (t0) cc_final: 0.7825 (p0) REVERT: C 449 TRP cc_start: 0.7761 (t60) cc_final: 0.6855 (t60) REVERT: C 609 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8816 (tm-30) REVERT: C 610 HIS cc_start: 0.9078 (t-170) cc_final: 0.8754 (t-90) REVERT: C 612 LEU cc_start: 0.8869 (tt) cc_final: 0.8380 (tt) REVERT: C 660 MET cc_start: 0.9084 (mmm) cc_final: 0.8684 (mmt) REVERT: C 664 ARG cc_start: 0.9043 (ptt180) cc_final: 0.8723 (ppt170) REVERT: C 720 MET cc_start: 0.7622 (mtp) cc_final: 0.6936 (ptm) REVERT: D 190 MET cc_start: 0.8150 (mmm) cc_final: 0.7599 (mmm) REVERT: D 238 LYS cc_start: 0.8916 (tttm) cc_final: 0.8677 (tptp) REVERT: D 334 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7768 (m90) REVERT: D 400 GLU cc_start: 0.9366 (tt0) cc_final: 0.8836 (tt0) REVERT: D 449 TRP cc_start: 0.7897 (t60) cc_final: 0.7003 (t60) REVERT: D 540 LYS cc_start: 0.9470 (ptpp) cc_final: 0.9246 (ptpp) REVERT: D 588 LEU cc_start: 0.8809 (mp) cc_final: 0.8523 (mm) REVERT: D 593 TYR cc_start: 0.7931 (m-80) cc_final: 0.7328 (m-80) REVERT: D 609 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8488 (tp30) REVERT: D 610 HIS cc_start: 0.9058 (t-170) cc_final: 0.8759 (t-90) REVERT: D 664 ARG cc_start: 0.9105 (ptt180) cc_final: 0.8560 (ppt170) REVERT: D 702 ASN cc_start: 0.9166 (m110) cc_final: 0.8685 (p0) REVERT: E 126 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7449 (tppt) REVERT: E 154 MET cc_start: 0.7489 (tmm) cc_final: 0.7085 (ppp) REVERT: E 186 TYR cc_start: 0.8985 (t80) cc_final: 0.8599 (t80) REVERT: E 208 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7287 (t80) REVERT: E 242 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8250 (mmtt) REVERT: E 295 MET cc_start: 0.8930 (tpt) cc_final: 0.8623 (ptm) REVERT: E 416 ARG cc_start: 0.9198 (mmm160) cc_final: 0.8620 (mmm160) REVERT: E 452 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.5817 (pt) REVERT: E 545 PHE cc_start: 0.9100 (m-80) cc_final: 0.8792 (m-80) REVERT: E 549 ARG cc_start: 0.9098 (mtt-85) cc_final: 0.8661 (tpp80) REVERT: E 668 GLN cc_start: 0.9088 (mm110) cc_final: 0.8769 (mm-40) REVERT: E 947 PHE cc_start: 0.9126 (m-80) cc_final: 0.8677 (m-80) REVERT: E 1099 LEU cc_start: 0.9420 (mt) cc_final: 0.9075 (pp) REVERT: E 1106 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8432 (mmt-90) REVERT: E 1126 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6580 (tm) REVERT: E 1134 LYS cc_start: 0.8088 (tttp) cc_final: 0.7831 (tptt) REVERT: E 1245 TYR cc_start: 0.9062 (m-80) cc_final: 0.8761 (m-80) REVERT: E 1353 PHE cc_start: 0.9189 (m-10) cc_final: 0.8782 (m-80) REVERT: E 1503 MET cc_start: 0.8901 (ttm) cc_final: 0.8602 (ttp) REVERT: E 1536 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8226 (t) REVERT: E 1574 ASN cc_start: 0.8771 (m-40) cc_final: 0.8454 (m110) REVERT: E 1615 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (mt) REVERT: E 1622 MET cc_start: 0.8054 (tpt) cc_final: 0.7391 (tpt) REVERT: E 1666 ILE cc_start: 0.9087 (pp) cc_final: 0.8862 (pp) REVERT: E 1704 ASP cc_start: 0.9146 (p0) cc_final: 0.8922 (p0) REVERT: E 2040 PHE cc_start: 0.6774 (m-80) cc_final: 0.6486 (m-80) REVERT: E 2065 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7859 (tp) REVERT: E 2093 PHE cc_start: 0.9304 (t80) cc_final: 0.9031 (t80) REVERT: E 2210 TYR cc_start: 0.8636 (t80) cc_final: 0.8169 (t80) REVERT: E 2222 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7645 (tt) REVERT: E 2247 LEU cc_start: 0.8681 (mt) cc_final: 0.8170 (mp) REVERT: E 2263 ARG cc_start: 0.5017 (tpm170) cc_final: 0.3890 (tpm170) REVERT: E 2282 LYS cc_start: 0.9259 (tttm) cc_final: 0.8845 (mtpp) REVERT: E 2304 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 2344 THR cc_start: 0.7849 (p) cc_final: 0.7085 (p) REVERT: E 2350 GLU cc_start: 0.8703 (tt0) cc_final: 0.8470 (pt0) outliers start: 216 outliers final: 140 residues processed: 975 average time/residue: 0.5522 time to fit residues: 902.9938 Evaluate side-chains 934 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 770 time to evaluate : 4.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 884 PHE Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1510 SER Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1536 SER Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1615 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 1906 SER Chi-restraints excluded: chain F residue 2008 MET Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2089 GLN Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2291 LEU Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 596 GLN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1373 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1506 HIS Chi-restraints excluded: chain E residue 1510 SER Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1615 LEU Chi-restraints excluded: chain E residue 1621 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 1906 SER Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2111 SER Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2222 LEU Chi-restraints excluded: chain E residue 2226 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 315 optimal weight: 0.0060 chunk 404 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 465 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 551 optimal weight: 0.6980 chunk 345 optimal weight: 6.9990 chunk 336 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 GLN ** F 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 934 GLN ** F1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1785 GLN ** F1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN C 334 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 HIS ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 GLN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2192 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 47082 Z= 0.205 Angle : 0.813 17.400 63787 Z= 0.392 Chirality : 0.046 0.360 7342 Planarity : 0.004 0.051 8019 Dihedral : 7.043 179.495 6244 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.20 % Allowed : 23.05 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 5688 helix: -0.37 (0.09), residues: 3550 sheet: -1.76 (0.46), residues: 80 loop : -2.81 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F2364 HIS 0.006 0.001 HIS F 118 PHE 0.046 0.002 PHE F1837 TYR 0.039 0.002 TYR F 175 ARG 0.007 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 831 time to evaluate : 5.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 120 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8714 (tp) REVERT: F 154 MET cc_start: 0.8068 (tmm) cc_final: 0.7257 (ppp) REVERT: F 186 TYR cc_start: 0.9139 (t80) cc_final: 0.8722 (t80) REVERT: F 289 LEU cc_start: 0.4118 (OUTLIER) cc_final: 0.3503 (tt) REVERT: F 295 MET cc_start: 0.9015 (tpt) cc_final: 0.8364 (ptt) REVERT: F 307 ILE cc_start: 0.9447 (pt) cc_final: 0.9022 (mm) REVERT: F 416 ARG cc_start: 0.9437 (mmm160) cc_final: 0.8874 (mmm160) REVERT: F 484 MET cc_start: 0.8559 (mtt) cc_final: 0.8291 (mtt) REVERT: F 539 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9026 (mm) REVERT: F 671 ASN cc_start: 0.8798 (m-40) cc_final: 0.8370 (m110) REVERT: F 697 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8814 (mmtt) REVERT: F 718 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8629 (mmmm) REVERT: F 728 ILE cc_start: 0.9150 (pt) cc_final: 0.8913 (tp) REVERT: F 748 MET cc_start: 0.8640 (mpp) cc_final: 0.7905 (mpp) REVERT: F 759 MET cc_start: 0.9108 (tpp) cc_final: 0.8805 (tpp) REVERT: F 767 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8091 (p0) REVERT: F 947 PHE cc_start: 0.8919 (m-80) cc_final: 0.8511 (m-80) REVERT: F 983 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8209 (ptmt) REVERT: F 1020 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8205 (tt) REVERT: F 1060 GLN cc_start: 0.8817 (tp40) cc_final: 0.8114 (tp40) REVERT: F 1099 LEU cc_start: 0.9439 (mt) cc_final: 0.9135 (pp) REVERT: F 1118 LYS cc_start: 0.9347 (ptpt) cc_final: 0.9022 (ptpp) REVERT: F 1126 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6518 (tm) REVERT: F 1155 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: F 1245 TYR cc_start: 0.9134 (m-80) cc_final: 0.8906 (m-80) REVERT: F 1314 ASP cc_start: 0.9373 (t0) cc_final: 0.9115 (m-30) REVERT: F 1349 ILE cc_start: 0.9006 (mt) cc_final: 0.8801 (pt) REVERT: F 1353 PHE cc_start: 0.9237 (m-10) cc_final: 0.8898 (m-80) REVERT: F 1488 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8439 (pptt) REVERT: F 1527 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7067 (mp) REVERT: F 1574 ASN cc_start: 0.8711 (m110) cc_final: 0.8259 (m110) REVERT: F 1615 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8508 (mt) REVERT: F 1837 PHE cc_start: 0.8575 (m-80) cc_final: 0.8180 (m-80) REVERT: F 1890 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: F 1897 TRP cc_start: 0.7725 (m100) cc_final: 0.7358 (m100) REVERT: F 1920 MET cc_start: 0.9128 (mmm) cc_final: 0.8478 (tmm) REVERT: F 2008 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6810 (mmm) REVERT: F 2020 ARG cc_start: 0.8884 (ptt180) cc_final: 0.8619 (ttp-170) REVERT: F 2065 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7657 (tp) REVERT: F 2097 MET cc_start: 0.9415 (mmm) cc_final: 0.9209 (tpt) REVERT: F 2110 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7986 (mmm160) REVERT: F 2213 MET cc_start: 0.8382 (mmm) cc_final: 0.8167 (mmm) REVERT: F 2247 LEU cc_start: 0.8986 (mt) cc_final: 0.8622 (mp) REVERT: F 2263 ARG cc_start: 0.5251 (tmt-80) cc_final: 0.4776 (tpm170) REVERT: F 2282 LYS cc_start: 0.9309 (tttm) cc_final: 0.8865 (mtpp) REVERT: F 2304 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 190 MET cc_start: 0.8184 (mmm) cc_final: 0.7520 (mmm) REVERT: C 201 ASP cc_start: 0.9008 (t0) cc_final: 0.8804 (t0) REVERT: C 238 LYS cc_start: 0.8797 (tttm) cc_final: 0.8579 (tptp) REVERT: C 400 GLU cc_start: 0.9324 (tt0) cc_final: 0.8744 (tt0) REVERT: C 437 ASN cc_start: 0.8335 (t0) cc_final: 0.7918 (p0) REVERT: C 449 TRP cc_start: 0.7730 (t60) cc_final: 0.6838 (t60) REVERT: C 574 MET cc_start: 0.8324 (mmm) cc_final: 0.7831 (mpp) REVERT: C 609 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8672 (tm-30) REVERT: C 610 HIS cc_start: 0.9083 (t-170) cc_final: 0.8732 (t-90) REVERT: C 612 LEU cc_start: 0.8851 (tt) cc_final: 0.8411 (tt) REVERT: C 660 MET cc_start: 0.9108 (mmm) cc_final: 0.8742 (mmt) REVERT: C 664 ARG cc_start: 0.8977 (ptt180) cc_final: 0.8704 (ppt170) REVERT: C 720 MET cc_start: 0.7654 (mtp) cc_final: 0.6976 (ptt) REVERT: D 238 LYS cc_start: 0.8913 (tttm) cc_final: 0.8680 (tptp) REVERT: D 269 ARG cc_start: 0.9092 (mtp85) cc_final: 0.8653 (mmm-85) REVERT: D 335 HIS cc_start: 0.7492 (p-80) cc_final: 0.5976 (t-170) REVERT: D 400 GLU cc_start: 0.9345 (tt0) cc_final: 0.8738 (tt0) REVERT: D 449 TRP cc_start: 0.7812 (t60) cc_final: 0.7062 (t60) REVERT: D 561 MET cc_start: 0.8810 (mmm) cc_final: 0.8419 (tpt) REVERT: D 588 LEU cc_start: 0.8860 (mp) cc_final: 0.8635 (mm) REVERT: D 593 TYR cc_start: 0.8009 (m-80) cc_final: 0.7387 (m-80) REVERT: D 609 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8398 (tp30) REVERT: D 610 HIS cc_start: 0.9031 (t-170) cc_final: 0.8699 (t-170) REVERT: D 664 ARG cc_start: 0.9097 (ptt180) cc_final: 0.8567 (ppt170) REVERT: D 720 MET cc_start: 0.7703 (mtp) cc_final: 0.7388 (ptt) REVERT: E 126 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7455 (tppt) REVERT: E 186 TYR cc_start: 0.9038 (t80) cc_final: 0.8727 (t80) REVERT: E 208 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7253 (t80) REVERT: E 295 MET cc_start: 0.8950 (tpt) cc_final: 0.8651 (ptm) REVERT: E 416 ARG cc_start: 0.9201 (mmm160) cc_final: 0.8592 (mmm160) REVERT: E 469 GLU cc_start: 0.8820 (tp30) cc_final: 0.8499 (tp30) REVERT: E 549 ARG cc_start: 0.9096 (mtt-85) cc_final: 0.8715 (tpp80) REVERT: E 575 LYS cc_start: 0.8992 (tptt) cc_final: 0.8674 (tptm) REVERT: E 587 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (mt) REVERT: E 615 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8572 (tp) REVERT: E 631 TRP cc_start: 0.8930 (m100) cc_final: 0.8522 (m100) REVERT: E 668 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8645 (mm110) REVERT: E 947 PHE cc_start: 0.9107 (m-80) cc_final: 0.8656 (m-80) REVERT: E 1106 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8422 (mmt-90) REVERT: E 1126 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6480 (tm) REVERT: E 1134 LYS cc_start: 0.8085 (tttp) cc_final: 0.7805 (ptpt) REVERT: E 1245 TYR cc_start: 0.9084 (m-80) cc_final: 0.8774 (m-80) REVERT: E 1353 PHE cc_start: 0.9168 (m-10) cc_final: 0.8767 (m-80) REVERT: E 1485 VAL cc_start: 0.9468 (p) cc_final: 0.9186 (m) REVERT: E 1488 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8423 (pptt) REVERT: E 1503 MET cc_start: 0.8892 (ttm) cc_final: 0.8566 (ttp) REVERT: E 1536 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8168 (t) REVERT: E 1574 ASN cc_start: 0.8784 (m-40) cc_final: 0.8501 (m110) REVERT: E 1615 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8769 (mt) REVERT: E 1622 MET cc_start: 0.8054 (tpt) cc_final: 0.7412 (tpt) REVERT: E 1666 ILE cc_start: 0.9027 (pp) cc_final: 0.8805 (pp) REVERT: E 1704 ASP cc_start: 0.9128 (p0) cc_final: 0.8908 (p0) REVERT: E 2020 ARG cc_start: 0.8863 (ptt180) cc_final: 0.8574 (ttp-170) REVERT: E 2040 PHE cc_start: 0.6755 (m-80) cc_final: 0.6451 (m-80) REVERT: E 2065 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7906 (tp) REVERT: E 2093 PHE cc_start: 0.9285 (t80) cc_final: 0.8663 (t80) REVERT: E 2099 PHE cc_start: 0.9286 (t80) cc_final: 0.9067 (t80) REVERT: E 2210 TYR cc_start: 0.8632 (t80) cc_final: 0.8129 (t80) REVERT: E 2247 LEU cc_start: 0.8809 (mt) cc_final: 0.8402 (mp) REVERT: E 2263 ARG cc_start: 0.4982 (tpm170) cc_final: 0.3899 (tpm170) REVERT: E 2282 LYS cc_start: 0.9251 (tttm) cc_final: 0.8917 (mttm) REVERT: E 2289 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8920 (mm) REVERT: E 2292 MET cc_start: 0.8864 (ptp) cc_final: 0.8270 (ptp) REVERT: E 2301 ASN cc_start: 0.8692 (m110) cc_final: 0.8485 (p0) REVERT: E 2304 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8337 (tm-30) REVERT: E 2344 THR cc_start: 0.7725 (p) cc_final: 0.6970 (p) REVERT: E 2350 GLU cc_start: 0.8713 (tt0) cc_final: 0.8368 (pt0) outliers start: 210 outliers final: 133 residues processed: 970 average time/residue: 0.5606 time to fit residues: 918.3937 Evaluate side-chains 935 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 775 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 736 TYR Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 884 PHE Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1389 ASP Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1536 SER Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1615 LEU Chi-restraints excluded: chain F residue 1621 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1880 ASP Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 2008 MET Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2291 LEU Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 596 GLN Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 597 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 937 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1373 THR Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1615 LEU Chi-restraints excluded: chain E residue 1621 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2289 LEU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2355 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 350 optimal weight: 0.7980 chunk 375 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 433 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1785 GLN ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2092 GLN ** F2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 GLN E 149 HIS ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 GLN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2192 ASN E2356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47082 Z= 0.227 Angle : 0.837 18.320 63787 Z= 0.404 Chirality : 0.046 0.333 7342 Planarity : 0.004 0.052 8019 Dihedral : 7.019 178.455 6244 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.88 % Allowed : 23.76 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.11), residues: 5688 helix: -0.34 (0.09), residues: 3556 sheet: -1.72 (0.46), residues: 78 loop : -2.75 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E1897 HIS 0.014 0.001 HIS F1955 PHE 0.043 0.002 PHE F1837 TYR 0.039 0.002 TYR E 175 ARG 0.008 0.001 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 797 time to evaluate : 5.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 135 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8873 (p) REVERT: F 154 MET cc_start: 0.8139 (tmm) cc_final: 0.7333 (ppp) REVERT: F 186 TYR cc_start: 0.9115 (t80) cc_final: 0.8777 (t80) REVERT: F 211 PHE cc_start: 0.8081 (t80) cc_final: 0.7831 (t80) REVERT: F 289 LEU cc_start: 0.4138 (OUTLIER) cc_final: 0.3559 (tt) REVERT: F 295 MET cc_start: 0.9014 (tpt) cc_final: 0.8477 (ptm) REVERT: F 307 ILE cc_start: 0.9482 (pt) cc_final: 0.9075 (mm) REVERT: F 416 ARG cc_start: 0.9435 (mmm160) cc_final: 0.8844 (mmm160) REVERT: F 484 MET cc_start: 0.8561 (mtt) cc_final: 0.8327 (mtt) REVERT: F 539 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8991 (mt) REVERT: F 668 GLN cc_start: 0.9166 (tp40) cc_final: 0.8585 (tp-100) REVERT: F 671 ASN cc_start: 0.8867 (m-40) cc_final: 0.8407 (m110) REVERT: F 697 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8800 (mmtt) REVERT: F 718 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8616 (mmmm) REVERT: F 728 ILE cc_start: 0.9171 (pt) cc_final: 0.8922 (tp) REVERT: F 748 MET cc_start: 0.8638 (mpp) cc_final: 0.8037 (mpp) REVERT: F 759 MET cc_start: 0.9119 (tpp) cc_final: 0.8861 (tpp) REVERT: F 767 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8119 (p0) REVERT: F 943 ARG cc_start: 0.8358 (mmt90) cc_final: 0.7704 (mmm-85) REVERT: F 947 PHE cc_start: 0.8965 (m-80) cc_final: 0.8062 (m-10) REVERT: F 983 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8357 (ptmt) REVERT: F 1020 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8214 (tt) REVERT: F 1036 ILE cc_start: 0.9063 (mm) cc_final: 0.8855 (mp) REVERT: F 1060 GLN cc_start: 0.8836 (tp40) cc_final: 0.8151 (tp40) REVERT: F 1106 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8456 (mmt180) REVERT: F 1118 LYS cc_start: 0.9355 (ptpt) cc_final: 0.9041 (ptpp) REVERT: F 1126 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6612 (tm) REVERT: F 1155 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: F 1245 TYR cc_start: 0.9141 (m-80) cc_final: 0.8910 (m-80) REVERT: F 1353 PHE cc_start: 0.9265 (m-10) cc_final: 0.8888 (m-80) REVERT: F 1488 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (pptt) REVERT: F 1527 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7077 (mp) REVERT: F 1574 ASN cc_start: 0.8748 (m110) cc_final: 0.8291 (m110) REVERT: F 1837 PHE cc_start: 0.8621 (m-80) cc_final: 0.8204 (m-80) REVERT: F 1890 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: F 1897 TRP cc_start: 0.7624 (m100) cc_final: 0.7399 (m100) REVERT: F 2008 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.6871 (mmm) REVERT: F 2020 ARG cc_start: 0.8932 (ptt180) cc_final: 0.8705 (ttp-170) REVERT: F 2065 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7742 (tp) REVERT: F 2093 PHE cc_start: 0.9356 (t80) cc_final: 0.8548 (t80) REVERT: F 2097 MET cc_start: 0.9438 (mmm) cc_final: 0.9068 (tpt) REVERT: F 2110 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8019 (mmm160) REVERT: F 2213 MET cc_start: 0.8418 (mmm) cc_final: 0.8186 (mmm) REVERT: F 2247 LEU cc_start: 0.9006 (mt) cc_final: 0.8648 (mp) REVERT: F 2263 ARG cc_start: 0.5236 (tmt-80) cc_final: 0.5001 (tpm170) REVERT: F 2282 LYS cc_start: 0.9385 (tttm) cc_final: 0.8938 (mttm) REVERT: F 2357 LEU cc_start: 0.8991 (mt) cc_final: 0.8754 (pp) REVERT: C 190 MET cc_start: 0.8196 (mmm) cc_final: 0.7711 (mmm) REVERT: C 201 ASP cc_start: 0.9044 (t0) cc_final: 0.8728 (m-30) REVERT: C 238 LYS cc_start: 0.8806 (tttm) cc_final: 0.8601 (tptp) REVERT: C 400 GLU cc_start: 0.9314 (tt0) cc_final: 0.8749 (tt0) REVERT: C 437 ASN cc_start: 0.8359 (t0) cc_final: 0.7934 (p0) REVERT: C 449 TRP cc_start: 0.7548 (t60) cc_final: 0.6617 (t60) REVERT: C 540 LYS cc_start: 0.9462 (ptpp) cc_final: 0.9251 (ptpp) REVERT: C 574 MET cc_start: 0.8225 (mmm) cc_final: 0.7849 (mpp) REVERT: C 609 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8715 (tm-30) REVERT: C 610 HIS cc_start: 0.9106 (t-170) cc_final: 0.8745 (t-90) REVERT: C 612 LEU cc_start: 0.8911 (tt) cc_final: 0.8709 (tt) REVERT: C 660 MET cc_start: 0.9076 (mmm) cc_final: 0.8755 (mmt) REVERT: C 664 ARG cc_start: 0.9004 (ptt180) cc_final: 0.8741 (ppt170) REVERT: C 720 MET cc_start: 0.7679 (mtp) cc_final: 0.7019 (ptm) REVERT: D 238 LYS cc_start: 0.8941 (tttm) cc_final: 0.8713 (tptp) REVERT: D 269 ARG cc_start: 0.9122 (mtp85) cc_final: 0.8692 (mmm-85) REVERT: D 335 HIS cc_start: 0.7398 (p-80) cc_final: 0.5857 (t-170) REVERT: D 400 GLU cc_start: 0.9332 (tt0) cc_final: 0.8767 (tt0) REVERT: D 449 TRP cc_start: 0.7842 (t60) cc_final: 0.6879 (t60) REVERT: D 540 LYS cc_start: 0.9460 (ptpp) cc_final: 0.9247 (ptpp) REVERT: D 588 LEU cc_start: 0.8876 (mp) cc_final: 0.8672 (mm) REVERT: D 593 TYR cc_start: 0.8039 (m-80) cc_final: 0.7499 (m-80) REVERT: D 609 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8429 (tp30) REVERT: D 610 HIS cc_start: 0.9055 (t-170) cc_final: 0.8730 (t-170) REVERT: D 660 MET cc_start: 0.8352 (mmt) cc_final: 0.8087 (mpp) REVERT: D 664 ARG cc_start: 0.9044 (ptt180) cc_final: 0.8767 (ppt170) REVERT: D 720 MET cc_start: 0.7723 (mtp) cc_final: 0.7391 (ptt) REVERT: E 126 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7816 (mtmt) REVERT: E 154 MET cc_start: 0.7713 (tmm) cc_final: 0.6733 (ppp) REVERT: E 173 LYS cc_start: 0.8672 (tttp) cc_final: 0.8234 (mmtm) REVERT: E 208 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7248 (t80) REVERT: E 295 MET cc_start: 0.8996 (tpt) cc_final: 0.8667 (ptm) REVERT: E 416 ARG cc_start: 0.9234 (mmm160) cc_final: 0.8697 (mmm160) REVERT: E 469 GLU cc_start: 0.8857 (tp30) cc_final: 0.8533 (tp30) REVERT: E 549 ARG cc_start: 0.9000 (mtt-85) cc_final: 0.8700 (tpp80) REVERT: E 575 LYS cc_start: 0.9043 (tptt) cc_final: 0.8739 (tptm) REVERT: E 615 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8424 (tp) REVERT: E 631 TRP cc_start: 0.9014 (m100) cc_final: 0.8559 (m100) REVERT: E 947 PHE cc_start: 0.9145 (m-80) cc_final: 0.8699 (m-80) REVERT: E 1099 LEU cc_start: 0.9402 (mt) cc_final: 0.9043 (pp) REVERT: E 1106 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8456 (mmt180) REVERT: E 1126 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6496 (tm) REVERT: E 1134 LYS cc_start: 0.8147 (tttp) cc_final: 0.7834 (ptpt) REVERT: E 1488 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8407 (pptt) REVERT: E 1503 MET cc_start: 0.8911 (ttm) cc_final: 0.8604 (ttp) REVERT: E 1536 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8243 (t) REVERT: E 1574 ASN cc_start: 0.8821 (m-40) cc_final: 0.8518 (m110) REVERT: E 1622 MET cc_start: 0.8028 (tpt) cc_final: 0.7366 (tpt) REVERT: E 1666 ILE cc_start: 0.9006 (pp) cc_final: 0.8786 (pp) REVERT: E 1704 ASP cc_start: 0.9072 (p0) cc_final: 0.8856 (p0) REVERT: E 1837 PHE cc_start: 0.8384 (m-10) cc_final: 0.8177 (m-80) REVERT: E 2020 ARG cc_start: 0.8777 (ptt180) cc_final: 0.8505 (ttp-170) REVERT: E 2040 PHE cc_start: 0.6799 (m-80) cc_final: 0.6501 (m-80) REVERT: E 2065 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7966 (tp) REVERT: E 2093 PHE cc_start: 0.9344 (t80) cc_final: 0.8686 (t80) REVERT: E 2099 PHE cc_start: 0.9304 (t80) cc_final: 0.9060 (t80) REVERT: E 2210 TYR cc_start: 0.8650 (t80) cc_final: 0.8233 (t80) REVERT: E 2247 LEU cc_start: 0.8808 (mt) cc_final: 0.8414 (mp) REVERT: E 2263 ARG cc_start: 0.5143 (tpm170) cc_final: 0.4431 (tpm170) REVERT: E 2282 LYS cc_start: 0.9250 (tttm) cc_final: 0.8925 (mttm) REVERT: E 2301 ASN cc_start: 0.8724 (m110) cc_final: 0.8466 (p0) REVERT: E 2304 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8300 (tm-30) REVERT: E 2344 THR cc_start: 0.7730 (p) cc_final: 0.6955 (p) REVERT: E 2350 GLU cc_start: 0.8694 (tt0) cc_final: 0.8424 (pt0) outliers start: 194 outliers final: 142 residues processed: 920 average time/residue: 0.6059 time to fit residues: 944.2582 Evaluate side-chains 923 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 757 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 654 PHE Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 736 TYR Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1389 ASP Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1510 SER Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1536 SER Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1621 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1880 ASP Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 2008 MET Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2291 LEU Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 596 GLN Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 597 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 937 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1165 VAL Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1373 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1510 SER Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1621 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2222 LEU Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2355 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 0.9990 chunk 528 optimal weight: 8.9990 chunk 481 optimal weight: 0.9990 chunk 513 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 403 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 464 optimal weight: 4.9990 chunk 485 optimal weight: 0.9980 chunk 511 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 GLN ** F 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1235 GLN ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN C 334 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 GLN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1785 GLN ** E1945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2192 ASN E2356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 47082 Z= 0.224 Angle : 0.842 16.765 63787 Z= 0.405 Chirality : 0.047 0.346 7342 Planarity : 0.004 0.051 8019 Dihedral : 6.998 178.674 6244 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.86 % Allowed : 24.21 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5688 helix: -0.34 (0.09), residues: 3540 sheet: -1.48 (0.48), residues: 78 loop : -2.73 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E1897 HIS 0.021 0.001 HIS C 334 PHE 0.042 0.002 PHE F1837 TYR 0.050 0.002 TYR E1355 ARG 0.008 0.001 ARG E 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 789 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 106 PHE cc_start: 0.8246 (t80) cc_final: 0.8043 (t80) REVERT: F 123 MET cc_start: 0.8896 (ttm) cc_final: 0.8636 (ttp) REVERT: F 135 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8891 (p) REVERT: F 154 MET cc_start: 0.8132 (tmm) cc_final: 0.7324 (ppp) REVERT: F 186 TYR cc_start: 0.9100 (t80) cc_final: 0.8824 (t80) REVERT: F 211 PHE cc_start: 0.8098 (t80) cc_final: 0.7865 (t80) REVERT: F 289 LEU cc_start: 0.4074 (OUTLIER) cc_final: 0.3350 (tt) REVERT: F 295 MET cc_start: 0.8991 (tpt) cc_final: 0.8545 (ptm) REVERT: F 307 ILE cc_start: 0.9478 (pt) cc_final: 0.9085 (mm) REVERT: F 416 ARG cc_start: 0.9435 (mmm160) cc_final: 0.8853 (mmm160) REVERT: F 452 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.5899 (pt) REVERT: F 484 MET cc_start: 0.8514 (mtt) cc_final: 0.8277 (mtt) REVERT: F 539 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9034 (mt) REVERT: F 590 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8468 (mtm-85) REVERT: F 668 GLN cc_start: 0.9207 (tp40) cc_final: 0.8611 (tp-100) REVERT: F 671 ASN cc_start: 0.8893 (m-40) cc_final: 0.8426 (m110) REVERT: F 697 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8761 (mmtt) REVERT: F 718 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8530 (mmmm) REVERT: F 728 ILE cc_start: 0.9168 (pt) cc_final: 0.8942 (tp) REVERT: F 748 MET cc_start: 0.8618 (mpp) cc_final: 0.7913 (mpp) REVERT: F 759 MET cc_start: 0.9113 (tpp) cc_final: 0.8834 (tpp) REVERT: F 767 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8187 (p0) REVERT: F 943 ARG cc_start: 0.8375 (mmt90) cc_final: 0.7703 (mmm-85) REVERT: F 947 PHE cc_start: 0.8964 (m-80) cc_final: 0.8061 (m-10) REVERT: F 983 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8421 (ptmt) REVERT: F 1020 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8292 (tt) REVERT: F 1060 GLN cc_start: 0.8835 (tp40) cc_final: 0.8164 (tp40) REVERT: F 1099 LEU cc_start: 0.9445 (mt) cc_final: 0.9136 (pp) REVERT: F 1106 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8406 (mmt180) REVERT: F 1118 LYS cc_start: 0.9349 (ptpt) cc_final: 0.9059 (ptpp) REVERT: F 1126 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6607 (tm) REVERT: F 1155 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: F 1245 TYR cc_start: 0.9141 (m-80) cc_final: 0.8911 (m-80) REVERT: F 1314 ASP cc_start: 0.9383 (t0) cc_final: 0.8944 (m-30) REVERT: F 1353 PHE cc_start: 0.9227 (m-10) cc_final: 0.8842 (m-80) REVERT: F 1488 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8262 (pptt) REVERT: F 1503 MET cc_start: 0.8540 (ttm) cc_final: 0.8280 (ptm) REVERT: F 1527 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7068 (mp) REVERT: F 1574 ASN cc_start: 0.8761 (m110) cc_final: 0.8317 (m110) REVERT: F 1837 PHE cc_start: 0.8621 (m-80) cc_final: 0.8326 (m-80) REVERT: F 1890 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: F 1897 TRP cc_start: 0.7725 (m100) cc_final: 0.7478 (m100) REVERT: F 2008 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7094 (mmm) REVERT: F 2020 ARG cc_start: 0.8921 (ptt180) cc_final: 0.8636 (ttp-170) REVERT: F 2065 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7704 (tp) REVERT: F 2093 PHE cc_start: 0.9352 (t80) cc_final: 0.8543 (t80) REVERT: F 2097 MET cc_start: 0.9446 (mmm) cc_final: 0.9077 (tpt) REVERT: F 2110 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8009 (mmm160) REVERT: F 2213 MET cc_start: 0.8430 (mmm) cc_final: 0.8171 (mmm) REVERT: F 2247 LEU cc_start: 0.9030 (mt) cc_final: 0.8678 (mp) REVERT: F 2263 ARG cc_start: 0.5211 (tmt-80) cc_final: 0.4896 (tpm170) REVERT: F 2282 LYS cc_start: 0.9378 (tttm) cc_final: 0.8966 (mttp) REVERT: F 2301 ASN cc_start: 0.8671 (m110) cc_final: 0.8288 (p0) REVERT: F 2357 LEU cc_start: 0.9005 (mt) cc_final: 0.8755 (pp) REVERT: C 201 ASP cc_start: 0.9068 (t0) cc_final: 0.8846 (t0) REVERT: C 238 LYS cc_start: 0.8812 (tttm) cc_final: 0.8594 (tptp) REVERT: C 400 GLU cc_start: 0.9294 (tt0) cc_final: 0.8704 (tt0) REVERT: C 437 ASN cc_start: 0.8449 (t0) cc_final: 0.8085 (p0) REVERT: C 449 TRP cc_start: 0.7529 (t60) cc_final: 0.6568 (t60) REVERT: C 540 LYS cc_start: 0.9462 (ptpp) cc_final: 0.9257 (ptpp) REVERT: C 574 MET cc_start: 0.8281 (mmm) cc_final: 0.7876 (mpp) REVERT: C 609 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8707 (tm-30) REVERT: C 610 HIS cc_start: 0.9106 (t-170) cc_final: 0.8757 (t-90) REVERT: C 660 MET cc_start: 0.9046 (mmm) cc_final: 0.8744 (mmt) REVERT: C 664 ARG cc_start: 0.9020 (ptt180) cc_final: 0.8733 (ppt170) REVERT: C 720 MET cc_start: 0.7685 (mtp) cc_final: 0.7027 (ptm) REVERT: D 238 LYS cc_start: 0.8927 (tttm) cc_final: 0.8677 (tptp) REVERT: D 269 ARG cc_start: 0.9114 (mtp85) cc_final: 0.8681 (mmm-85) REVERT: D 400 GLU cc_start: 0.9334 (tt0) cc_final: 0.8764 (tt0) REVERT: D 449 TRP cc_start: 0.7721 (t60) cc_final: 0.6719 (t60) REVERT: D 593 TYR cc_start: 0.8131 (m-80) cc_final: 0.7564 (m-80) REVERT: D 609 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8428 (tp30) REVERT: D 610 HIS cc_start: 0.9080 (t-170) cc_final: 0.8795 (t-170) REVERT: D 720 MET cc_start: 0.7739 (mtp) cc_final: 0.7390 (ptt) REVERT: E 126 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7813 (mtmt) REVERT: E 140 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8106 (mmtp) REVERT: E 154 MET cc_start: 0.7670 (tmm) cc_final: 0.6712 (ppp) REVERT: E 186 TYR cc_start: 0.8933 (t80) cc_final: 0.8620 (t80) REVERT: E 208 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7190 (t80) REVERT: E 295 MET cc_start: 0.9051 (tpt) cc_final: 0.8711 (ptm) REVERT: E 416 ARG cc_start: 0.9317 (mmm160) cc_final: 0.8654 (mmm160) REVERT: E 469 GLU cc_start: 0.8897 (tp30) cc_final: 0.8557 (tp30) REVERT: E 575 LYS cc_start: 0.9019 (tptt) cc_final: 0.8658 (tttt) REVERT: E 615 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8475 (tp) REVERT: E 631 TRP cc_start: 0.9014 (m100) cc_final: 0.8593 (m100) REVERT: E 943 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8225 (mmt90) REVERT: E 947 PHE cc_start: 0.9144 (m-80) cc_final: 0.8661 (m-80) REVERT: E 1106 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8478 (mmt180) REVERT: E 1126 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6534 (tm) REVERT: E 1134 LYS cc_start: 0.8234 (tttp) cc_final: 0.7921 (ptpt) REVERT: E 1488 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8379 (pptt) REVERT: E 1503 MET cc_start: 0.8908 (ttm) cc_final: 0.8566 (ttp) REVERT: E 1536 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8244 (t) REVERT: E 1574 ASN cc_start: 0.8815 (m-40) cc_final: 0.8510 (m110) REVERT: E 1622 MET cc_start: 0.7960 (tpt) cc_final: 0.7364 (tpt) REVERT: E 1666 ILE cc_start: 0.9008 (pp) cc_final: 0.8789 (pp) REVERT: E 1704 ASP cc_start: 0.9012 (p0) cc_final: 0.8786 (p0) REVERT: E 1837 PHE cc_start: 0.8389 (m-10) cc_final: 0.8185 (m-80) REVERT: E 2020 ARG cc_start: 0.8777 (ptt180) cc_final: 0.8510 (ttp-170) REVERT: E 2040 PHE cc_start: 0.6783 (m-80) cc_final: 0.6465 (m-80) REVERT: E 2065 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8018 (tp) REVERT: E 2092 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8730 (tp-100) REVERT: E 2093 PHE cc_start: 0.9347 (t80) cc_final: 0.8701 (t80) REVERT: E 2282 LYS cc_start: 0.9270 (tttm) cc_final: 0.8952 (mttm) REVERT: E 2301 ASN cc_start: 0.8722 (m110) cc_final: 0.8473 (p0) REVERT: E 2304 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8293 (tm-30) REVERT: E 2344 THR cc_start: 0.7738 (p) cc_final: 0.7025 (p) REVERT: E 2350 GLU cc_start: 0.8652 (tt0) cc_final: 0.8409 (pt0) outliers start: 193 outliers final: 143 residues processed: 909 average time/residue: 0.5484 time to fit residues: 835.1499 Evaluate side-chains 926 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 758 time to evaluate : 5.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 654 PHE Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 736 TYR Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 770 GLN Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1621 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1880 ASP Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1906 SER Chi-restraints excluded: chain F residue 2008 MET Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 596 GLN Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 597 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 723 ILE Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 937 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1165 VAL Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1350 PHE Chi-restraints excluded: chain E residue 1373 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1510 SER Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1621 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1890 GLN Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2355 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 4.9990 chunk 543 optimal weight: 20.0000 chunk 331 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 377 optimal weight: 0.5980 chunk 569 optimal weight: 4.9990 chunk 524 optimal weight: 1.9990 chunk 453 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 350 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 GLN F 767 ASN F 770 GLN F 868 GLN ** F 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1785 GLN ** F1943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2187 GLN F2192 ASN C 334 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 GLN E1048 ASN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1507 GLN ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1604 ASN ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1785 GLN ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2177 GLN E2192 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47082 Z= 0.206 Angle : 0.862 17.396 63787 Z= 0.411 Chirality : 0.048 0.468 7342 Planarity : 0.004 0.049 8019 Dihedral : 6.962 179.505 6244 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.25 % Allowed : 25.00 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5688 helix: -0.35 (0.09), residues: 3556 sheet: -1.20 (0.51), residues: 78 loop : -2.73 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E1897 HIS 0.017 0.001 HIS C 334 PHE 0.042 0.002 PHE D 323 TYR 0.047 0.002 TYR E1355 ARG 0.008 0.000 ARG D 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 822 time to evaluate : 5.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 106 PHE cc_start: 0.8235 (t80) cc_final: 0.7992 (t80) REVERT: F 123 MET cc_start: 0.8887 (ttm) cc_final: 0.8585 (ttp) REVERT: F 135 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8878 (p) REVERT: F 154 MET cc_start: 0.8105 (tmm) cc_final: 0.7334 (ppp) REVERT: F 186 TYR cc_start: 0.9129 (t80) cc_final: 0.8867 (t80) REVERT: F 211 PHE cc_start: 0.8034 (t80) cc_final: 0.7795 (t80) REVERT: F 289 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3259 (tt) REVERT: F 295 MET cc_start: 0.8912 (tpt) cc_final: 0.8570 (ptm) REVERT: F 307 ILE cc_start: 0.9471 (pt) cc_final: 0.9075 (mm) REVERT: F 416 ARG cc_start: 0.9420 (mmm160) cc_final: 0.8848 (mmm160) REVERT: F 452 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.5890 (pt) REVERT: F 484 MET cc_start: 0.8516 (mtt) cc_final: 0.8255 (mtt) REVERT: F 539 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9116 (mm) REVERT: F 590 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8455 (mtm-85) REVERT: F 668 GLN cc_start: 0.9181 (tp40) cc_final: 0.8615 (tp-100) REVERT: F 671 ASN cc_start: 0.8858 (m-40) cc_final: 0.8443 (m-40) REVERT: F 728 ILE cc_start: 0.9161 (pt) cc_final: 0.8952 (tp) REVERT: F 748 MET cc_start: 0.8689 (mpp) cc_final: 0.8331 (mpp) REVERT: F 759 MET cc_start: 0.9101 (tpp) cc_final: 0.8890 (tpp) REVERT: F 947 PHE cc_start: 0.8928 (m-80) cc_final: 0.8617 (m-80) REVERT: F 983 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8356 (ptmt) REVERT: F 1020 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8352 (tt) REVERT: F 1036 ILE cc_start: 0.9007 (mm) cc_final: 0.8794 (mp) REVERT: F 1060 GLN cc_start: 0.8823 (tp40) cc_final: 0.8163 (tp40) REVERT: F 1099 LEU cc_start: 0.9449 (mt) cc_final: 0.9129 (pp) REVERT: F 1106 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8428 (mmt180) REVERT: F 1118 LYS cc_start: 0.9321 (ptpt) cc_final: 0.9045 (ptpp) REVERT: F 1126 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6583 (tm) REVERT: F 1155 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (m-80) REVERT: F 1245 TYR cc_start: 0.9101 (m-80) cc_final: 0.8864 (m-80) REVERT: F 1314 ASP cc_start: 0.9377 (t0) cc_final: 0.8952 (m-30) REVERT: F 1353 PHE cc_start: 0.9234 (m-10) cc_final: 0.8835 (m-80) REVERT: F 1488 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8305 (pptt) REVERT: F 1527 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7069 (mp) REVERT: F 1536 SER cc_start: 0.8753 (t) cc_final: 0.8450 (t) REVERT: F 1574 ASN cc_start: 0.8802 (m110) cc_final: 0.8387 (m110) REVERT: F 1837 PHE cc_start: 0.8585 (m-80) cc_final: 0.8149 (m-80) REVERT: F 1844 VAL cc_start: 0.9295 (m) cc_final: 0.8697 (m) REVERT: F 1897 TRP cc_start: 0.7682 (m100) cc_final: 0.7401 (m100) REVERT: F 2008 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7049 (mmm) REVERT: F 2020 ARG cc_start: 0.8889 (ptt180) cc_final: 0.8623 (ttp-170) REVERT: F 2065 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7779 (tp) REVERT: F 2089 GLN cc_start: 0.8713 (pt0) cc_final: 0.8378 (pm20) REVERT: F 2093 PHE cc_start: 0.9342 (t80) cc_final: 0.8569 (t80) REVERT: F 2097 MET cc_start: 0.9433 (mmm) cc_final: 0.9063 (tpt) REVERT: F 2110 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7903 (mmm160) REVERT: F 2213 MET cc_start: 0.8385 (mmm) cc_final: 0.8136 (mmm) REVERT: F 2247 LEU cc_start: 0.9074 (mt) cc_final: 0.8754 (mp) REVERT: F 2282 LYS cc_start: 0.9323 (tttm) cc_final: 0.8910 (mttp) REVERT: F 2301 ASN cc_start: 0.8663 (m110) cc_final: 0.8335 (p0) REVERT: C 269 ARG cc_start: 0.8392 (tpm170) cc_final: 0.7986 (tpm170) REVERT: C 400 GLU cc_start: 0.9286 (tt0) cc_final: 0.8619 (tt0) REVERT: C 437 ASN cc_start: 0.8475 (t0) cc_final: 0.8113 (p0) REVERT: C 449 TRP cc_start: 0.7550 (t60) cc_final: 0.6582 (t60) REVERT: C 476 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: C 574 MET cc_start: 0.8235 (mmm) cc_final: 0.7788 (mpp) REVERT: C 609 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8734 (tm-30) REVERT: C 610 HIS cc_start: 0.9076 (t-170) cc_final: 0.8731 (t-90) REVERT: C 660 MET cc_start: 0.9012 (mmm) cc_final: 0.8685 (mmt) REVERT: C 664 ARG cc_start: 0.9032 (ptt180) cc_final: 0.8686 (ppt170) REVERT: D 238 LYS cc_start: 0.8900 (tttm) cc_final: 0.8694 (tptp) REVERT: D 269 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8661 (mmm-85) REVERT: D 377 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.7598 (tpt90) REVERT: D 400 GLU cc_start: 0.9334 (tt0) cc_final: 0.8750 (tt0) REVERT: D 449 TRP cc_start: 0.7619 (t60) cc_final: 0.6640 (t60) REVERT: D 588 LEU cc_start: 0.8829 (mm) cc_final: 0.8502 (mm) REVERT: D 593 TYR cc_start: 0.8121 (m-80) cc_final: 0.7348 (m-10) REVERT: D 601 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9082 (mm) REVERT: D 609 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8448 (tp30) REVERT: D 610 HIS cc_start: 0.9037 (t-170) cc_final: 0.8701 (t-170) REVERT: D 660 MET cc_start: 0.8276 (mpp) cc_final: 0.8041 (mpp) REVERT: D 720 MET cc_start: 0.7715 (mtp) cc_final: 0.7349 (ptt) REVERT: E 154 MET cc_start: 0.7663 (tmm) cc_final: 0.6767 (ppp) REVERT: E 186 TYR cc_start: 0.8962 (t80) cc_final: 0.8666 (t80) REVERT: E 208 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7114 (t80) REVERT: E 295 MET cc_start: 0.9030 (tpt) cc_final: 0.8683 (ptm) REVERT: E 395 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9199 (tptp) REVERT: E 416 ARG cc_start: 0.9316 (mmm160) cc_final: 0.8671 (mmm160) REVERT: E 469 GLU cc_start: 0.8881 (tp30) cc_final: 0.8530 (tp30) REVERT: E 549 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8322 (tpp80) REVERT: E 575 LYS cc_start: 0.9006 (tptt) cc_final: 0.8494 (tptm) REVERT: E 615 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8435 (tp) REVERT: E 631 TRP cc_start: 0.9022 (m100) cc_final: 0.8589 (m100) REVERT: E 727 TYR cc_start: 0.7758 (m-80) cc_final: 0.7405 (m-80) REVERT: E 943 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8150 (mmt90) REVERT: E 947 PHE cc_start: 0.9094 (m-80) cc_final: 0.8623 (m-80) REVERT: E 1099 LEU cc_start: 0.9425 (mt) cc_final: 0.9041 (pp) REVERT: E 1106 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8479 (mmt180) REVERT: E 1126 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6431 (tm) REVERT: E 1134 LYS cc_start: 0.8270 (tttp) cc_final: 0.7953 (ptpt) REVERT: E 1488 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8451 (pptt) REVERT: E 1503 MET cc_start: 0.8874 (ttm) cc_final: 0.8559 (ttp) REVERT: E 1536 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8176 (t) REVERT: E 1574 ASN cc_start: 0.8725 (m-40) cc_final: 0.8436 (m110) REVERT: E 1622 MET cc_start: 0.7864 (tpt) cc_final: 0.7324 (tpt) REVERT: E 1666 ILE cc_start: 0.8975 (pp) cc_final: 0.8768 (pp) REVERT: E 1704 ASP cc_start: 0.9021 (p0) cc_final: 0.8804 (p0) REVERT: E 1837 PHE cc_start: 0.8362 (m-10) cc_final: 0.8145 (m-80) REVERT: E 2020 ARG cc_start: 0.8767 (ptt180) cc_final: 0.8509 (ttp-170) REVERT: E 2040 PHE cc_start: 0.6707 (m-80) cc_final: 0.6454 (m-80) REVERT: E 2065 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (tp) REVERT: E 2092 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8735 (tp-100) REVERT: E 2093 PHE cc_start: 0.9324 (t80) cc_final: 0.8707 (t80) REVERT: E 2174 TYR cc_start: 0.8474 (t80) cc_final: 0.8245 (t80) REVERT: E 2222 LEU cc_start: 0.8681 (mp) cc_final: 0.8318 (tp) REVERT: E 2247 LEU cc_start: 0.8944 (mt) cc_final: 0.8328 (mp) REVERT: E 2275 ILE cc_start: 0.8254 (pt) cc_final: 0.8021 (pt) REVERT: E 2282 LYS cc_start: 0.9250 (tttm) cc_final: 0.8941 (mttm) REVERT: E 2304 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8285 (tm-30) REVERT: E 2344 THR cc_start: 0.7712 (p) cc_final: 0.7036 (p) outliers start: 162 outliers final: 125 residues processed: 925 average time/residue: 0.5628 time to fit residues: 873.8438 Evaluate side-chains 934 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 785 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 LYS Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 635 THR Chi-restraints excluded: chain F residue 654 PHE Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1282 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1439 GLN Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1600 LEU Chi-restraints excluded: chain F residue 1621 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1724 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1880 ASP Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 2008 MET Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2110 ARG Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2171 LEU Chi-restraints excluded: chain F residue 2222 LEU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 596 GLN Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 635 THR Chi-restraints excluded: chain E residue 723 ILE Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 928 GLN Chi-restraints excluded: chain E residue 937 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1165 VAL Chi-restraints excluded: chain E residue 1282 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1350 PHE Chi-restraints excluded: chain E residue 1373 THR Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1510 SER Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1600 LEU Chi-restraints excluded: chain E residue 1621 LEU Chi-restraints excluded: chain E residue 1630 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1833 PHE Chi-restraints excluded: chain E residue 1902 THR Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2355 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 4.9990 chunk 483 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 418 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 chunk 454 optimal weight: 4.9990 chunk 190 optimal weight: 0.0270 chunk 466 optimal weight: 0.0050 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.9456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 GLN ** F 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1785 GLN ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2192 ASN F2356 ASN C 334 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 HIS ** E 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 GLN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2187 GLN E2192 ASN E2356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.083371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.067086 restraints weight = 283686.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.069360 restraints weight = 170772.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.071011 restraints weight = 116878.965| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 47082 Z= 0.224 Angle : 0.869 16.683 63787 Z= 0.417 Chirality : 0.048 0.450 7342 Planarity : 0.004 0.048 8019 Dihedral : 6.949 178.647 6244 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.27 % Allowed : 25.58 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.11), residues: 5688 helix: -0.36 (0.09), residues: 3526 sheet: -1.05 (0.55), residues: 78 loop : -2.70 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E1897 HIS 0.024 0.001 HIS F1955 PHE 0.040 0.002 PHE E1350 TYR 0.047 0.002 TYR E1355 ARG 0.008 0.000 ARG E 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15407.59 seconds wall clock time: 275 minutes 9.02 seconds (16509.02 seconds total)