Starting phenix.real_space_refine on Sun Feb 18 12:11:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwf_34311/02_2024/8gwf_34311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwf_34311/02_2024/8gwf_34311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwf_34311/02_2024/8gwf_34311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwf_34311/02_2024/8gwf_34311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwf_34311/02_2024/8gwf_34311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwf_34311/02_2024/8gwf_34311_updated.pdb" } resolution = 3.39 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= -0.000 sd= 0.031 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 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 583": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 542": "OD1" <-> "OD2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 75.578 55.650 121.844 1.00 86.97 S ATOM 2506 SG CYS A 306 75.567 57.180 125.354 1.00 84.94 S ATOM 2538 SG CYS A 310 76.856 53.605 124.773 1.00 84.77 S ATOM 3946 SG CYS A 487 78.264 69.779 106.107 1.00 95.87 S ATOM 5199 SG CYS A 645 77.470 71.834 109.252 1.00 97.77 S ATOM 5205 SG CYS A 646 76.146 68.218 108.904 1.00 89.00 S ATOM 12129 SG CYS F 16 102.478 65.216 50.524 1.00183.45 S ATOM 12144 SG CYS F 19 103.212 62.542 47.852 1.00198.14 S ATOM 12047 SG CYS F 5 114.925 66.378 50.337 1.00183.01 S ATOM 12068 SG CYS F 8 115.808 69.235 47.969 1.00185.13 S ATOM 12206 SG CYS F 26 114.614 70.148 51.170 1.00172.26 S ATOM 12223 SG CYS F 29 112.090 68.304 48.775 1.00175.19 S ATOM 12388 SG CYS F 50 93.154 76.836 65.675 1.00158.72 S ATOM 12418 SG CYS F 55 89.756 76.042 64.216 1.00164.97 S ATOM 12551 SG CYS F 72 91.926 78.390 62.448 1.00168.17 S ATOM 16642 SG CYS E 16 61.349 74.627 65.591 1.00165.58 S ATOM 16657 SG CYS E 19 58.755 72.126 64.275 1.00179.24 S ATOM 16560 SG CYS E 5 70.232 70.535 57.925 1.00188.71 S ATOM 16581 SG CYS E 8 70.961 72.499 54.838 1.00197.10 S ATOM 16719 SG CYS E 26 72.392 73.907 58.159 1.00186.39 S ATOM 16736 SG CYS E 29 68.780 74.086 57.029 1.00167.57 S ATOM 16901 SG CYS E 50 66.240 87.403 79.620 1.00176.08 S ATOM 16931 SG CYS E 55 63.011 88.887 81.055 1.00192.48 S ATOM 17064 SG CYS E 72 65.078 90.922 78.545 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 16.04, per 1000 atoms: 0.73 Number of scatterers: 21955 At special positions: 0 Unit cell: (154.98, 136.94, 186.14, 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 8 29.99 S 158 16.00 P 55 15.00 O 4305 8.00 N 3694 7.00 C 13735 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: 8.46 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 20 sheets defined 34.7% alpha, 7.9% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 9.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.911A pdb=" N PHE A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 8 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 11 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.612A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 199 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.325A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.760A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.645A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.597A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.182A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.033A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 641 removed outlier: 5.086A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 901 removed outlier: 3.921A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.608A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 919 through 925' Processing helix chain 'B' and resid 10 through 27 removed outlier: 4.743A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 97 removed outlier: 4.034A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.763A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.955A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.681A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 32 through 81 removed outlier: 4.449A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'F' and resid 27 through 35 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 128 through 146 Processing helix chain 'F' and resid 266 through 274 Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.684A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 426 through 432 removed outlier: 3.999A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 455 removed outlier: 4.410A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 504 through 506 No H-bonds generated for 'chain 'F' and resid 504 through 506' Processing helix chain 'F' and resid 517 through 524 removed outlier: 3.990A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 565 No H-bonds generated for 'chain 'F' and resid 562 through 565' Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 128 through 147 Processing helix chain 'E' and resid 265 through 272 Processing helix chain 'E' and resid 291 through 298 removed outlier: 3.748A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 removed outlier: 4.509A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 431 removed outlier: 3.864A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 455 Processing helix chain 'E' and resid 490 through 493 No H-bonds generated for 'chain 'E' and resid 490 through 493' Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'E' and resid 516 through 525 Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.513A pdb=" N THR E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 7.012A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.531A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 335 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.800A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 5.943A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.679A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 152 through 154 Processing sheet with id= L, first strand: chain 'F' and resid 370 through 373 removed outlier: 6.351A pdb=" N HIS F 395 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE F 373 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 397 " --> pdb=" O PHE F 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.672A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 395 through 398 removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 187 removed outlier: 4.126A pdb=" N GLY E 184 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 29 through 31 Processing sheet with id= S, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.737A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 73 through 76 removed outlier: 3.676A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 6.94 Time building geometry restraints manager: 9.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.45 - 0.72: 1 0.72 - 1.00: 0 1.00 - 1.27: 3471 1.27 - 1.54: 18641 1.54 - 1.82: 414 Warning: very small bond lengths. Bond restraints: 22527 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.448 1.055 3.40e-02 8.65e+02 9.63e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.632 -0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.94e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.66e+01 bond pdb=" N ALA G 15 " pdb=" CA ALA G 15 " ideal model delta sigma weight residual 1.458 1.541 -0.083 1.27e-02 6.20e+03 4.32e+01 ... (remaining 22522 not shown) Histogram of bond angle deviations from ideal: 68.93 - 82.89: 2 82.89 - 96.85: 6 96.85 - 110.81: 8020 110.81 - 124.77: 22351 124.77 - 138.73: 500 Bond angle restraints: 30879 Sorted by residual: angle pdb=" N PRO F 491 " pdb=" CD PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 103.20 68.93 34.27 1.50e+00 4.44e-01 5.22e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.87 22.13 1.40e+00 5.10e-01 2.50e+02 angle pdb=" CA PRO F 491 " pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 112.00 90.72 21.28 1.40e+00 5.10e-01 2.31e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.73 -27.93 2.13e+00 2.20e-01 1.72e+02 angle pdb=" CA PRO F 491 " pdb=" CB PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 104.50 80.58 23.92 1.90e+00 2.77e-01 1.58e+02 ... (remaining 30874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 12788 33.29 - 66.58: 741 66.58 - 99.87: 35 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13566 sinusoidal: 5672 harmonic: 7894 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.42 -36.62 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.49 35.89 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.41 -24.61 0 2.50e+00 1.60e-01 9.69e+01 ... (remaining 13563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 310 2.62 - 3.19: 18733 3.19 - 3.76: 34253 3.76 - 4.33: 46531 4.33 - 4.90: 74441 Nonbonded interactions: 174268 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 2.440 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 2.440 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 2.440 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 2.440 ... (remaining 174263 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 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } 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=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.610 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: 0.020 Extract box with map and model: 19.390 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 73.520 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.009 1.055 22527 Z= 0.479 Angle : 0.940 34.266 30879 Z= 0.545 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.826 166.450 8472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % 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: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 PHE 0.017 0.001 PHE F 437 TYR 0.022 0.001 TYR F 299 ARG 0.006 0.001 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 296 time to evaluate : 2.363 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: A 50 LYS cc_start: 0.7063 (tptt) cc_final: 0.6792 (tptp) REVERT: A 114 ILE cc_start: 0.5885 (mt) cc_final: 0.5594 (mt) REVERT: A 115 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7119 (m) REVERT: A 161 ASP cc_start: 0.7922 (m-30) cc_final: 0.7523 (m-30) REVERT: A 258 ASP cc_start: 0.8608 (m-30) cc_final: 0.8172 (t0) REVERT: A 366 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7602 (pp) REVERT: A 499 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: A 607 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 665 GLU cc_start: 0.8760 (pm20) cc_final: 0.8497 (pm20) REVERT: B 135 TYR cc_start: 0.8245 (t80) cc_final: 0.8039 (t80) REVERT: C 15 SER cc_start: 0.8832 (t) cc_final: 0.8084 (m) REVERT: F 9 ASN cc_start: 0.7774 (t0) cc_final: 0.7491 (m-40) REVERT: F 68 MET cc_start: 0.7886 (mtm) cc_final: 0.6658 (mmt) REVERT: F 453 SER cc_start: 0.1031 (OUTLIER) cc_final: 0.0655 (t) REVERT: F 544 VAL cc_start: 0.0757 (OUTLIER) cc_final: 0.0246 (t) REVERT: F 576 MET cc_start: -0.0071 (mmt) cc_final: -0.2126 (mtt) REVERT: E 233 MET cc_start: 0.7716 (mpm) cc_final: 0.6808 (tpp) REVERT: E 315 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8439 (p0) REVERT: G 46 SER cc_start: 0.6456 (OUTLIER) cc_final: 0.5763 (t) outliers start: 116 outliers final: 27 residues processed: 398 average time/residue: 0.3672 time to fit residues: 219.4193 Evaluate side-chains 195 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 168 ASN B 73 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN D 176 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN F 388 ASN E 116 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 22527 Z= 0.241 Angle : 0.693 15.690 30879 Z= 0.353 Chirality : 0.044 0.284 3581 Planarity : 0.005 0.058 3748 Dihedral : 12.905 150.776 3781 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.47 % Favored : 91.26 % Rotamer: Outliers : 5.09 % Allowed : 31.04 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.80 (0.16), residues: 2650 helix: 0.28 (0.17), residues: 959 sheet: -1.07 (0.34), residues: 240 loop : -2.35 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 182 HIS 0.007 0.001 HIS E 554 PHE 0.023 0.002 PHE F 373 TYR 0.019 0.002 TYR A 237 ARG 0.007 0.001 ARG F 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 170 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.6641 (tptt) cc_final: 0.6368 (tptp) REVERT: A 110 MET cc_start: 0.7596 (tpp) cc_final: 0.7228 (tpp) REVERT: A 114 ILE cc_start: 0.7190 (mt) cc_final: 0.6920 (mt) REVERT: A 258 ASP cc_start: 0.8573 (m-30) cc_final: 0.8200 (t0) REVERT: A 665 GLU cc_start: 0.8831 (pm20) cc_final: 0.8506 (pm20) REVERT: A 924 MET cc_start: 0.8781 (mmm) cc_final: 0.8285 (mtt) REVERT: B 62 MET cc_start: 0.8270 (ttt) cc_final: 0.7898 (tpp) REVERT: B 75 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8370 (ttp80) REVERT: B 174 MET cc_start: 0.9039 (tpp) cc_final: 0.8770 (tpp) REVERT: C 38 ASP cc_start: 0.8624 (t0) cc_final: 0.8403 (t0) REVERT: D 60 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7900 (pp20) REVERT: F 9 ASN cc_start: 0.8005 (t0) cc_final: 0.7790 (m-40) REVERT: F 68 MET cc_start: 0.8102 (mtm) cc_final: 0.6808 (mmt) REVERT: F 185 TYR cc_start: 0.8224 (p90) cc_final: 0.7920 (p90) REVERT: F 531 GLN cc_start: -0.0224 (OUTLIER) cc_final: -0.0813 (mm-40) REVERT: F 576 MET cc_start: -0.0104 (mmt) cc_final: -0.2143 (mtt) REVERT: E 233 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7022 (tpp) REVERT: E 274 MET cc_start: 0.8111 (mmm) cc_final: 0.7221 (mmp) REVERT: E 554 HIS cc_start: 0.3516 (OUTLIER) cc_final: 0.2709 (t-90) REVERT: G 2 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8288 (m-40) outliers start: 115 outliers final: 49 residues processed: 273 average time/residue: 0.3605 time to fit residues: 152.0661 Evaluate side-chains 192 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 139 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 242 optimal weight: 30.0000 chunk 262 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 HIS A 489 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 164 HIS F 265 ASN F 388 ASN F 492 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 22527 Z= 0.431 Angle : 0.754 9.295 30879 Z= 0.392 Chirality : 0.047 0.269 3581 Planarity : 0.005 0.056 3748 Dihedral : 12.826 139.065 3755 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.11 % Favored : 90.62 % Rotamer: Outliers : 6.15 % Allowed : 30.38 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.08 (0.16), residues: 2650 helix: -0.13 (0.17), residues: 955 sheet: -1.25 (0.36), residues: 210 loop : -2.35 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 916 HIS 0.016 0.002 HIS E 554 PHE 0.035 0.003 PHE A 102 TYR 0.022 0.002 TYR A 884 ARG 0.008 0.001 ARG G 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 138 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8842 (p0) REVERT: A 61 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8646 (pm20) REVERT: A 110 MET cc_start: 0.7947 (tpp) cc_final: 0.7668 (tpp) REVERT: A 167 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8223 (pp20) REVERT: A 258 ASP cc_start: 0.8711 (m-30) cc_final: 0.8490 (t0) REVERT: A 924 MET cc_start: 0.8888 (mmm) cc_final: 0.8526 (mtt) REVERT: C 38 ASP cc_start: 0.9003 (t0) cc_final: 0.8736 (t0) REVERT: F 9 ASN cc_start: 0.8266 (t0) cc_final: 0.8047 (m-40) REVERT: F 68 MET cc_start: 0.8270 (mtm) cc_final: 0.7113 (mmt) REVERT: F 185 TYR cc_start: 0.8380 (p90) cc_final: 0.8089 (p90) REVERT: F 490 ARG cc_start: -0.0612 (OUTLIER) cc_final: -0.1322 (mtm-85) REVERT: F 531 GLN cc_start: -0.0281 (OUTLIER) cc_final: -0.0845 (mm-40) REVERT: F 552 THR cc_start: 0.4747 (OUTLIER) cc_final: 0.4491 (t) REVERT: F 576 MET cc_start: 0.0011 (mmt) cc_final: -0.2328 (mtt) REVERT: E 185 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7129 (t80) REVERT: E 233 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7309 (tpp) REVERT: E 274 MET cc_start: 0.8295 (mmm) cc_final: 0.7891 (mmm) REVERT: E 475 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4530 (p90) REVERT: E 554 HIS cc_start: 0.3002 (OUTLIER) cc_final: 0.1709 (t-170) REVERT: E 576 MET cc_start: -0.3361 (tmm) cc_final: -0.3705 (ttp) REVERT: G 74 ARG cc_start: 0.8304 (ptm-80) cc_final: 0.7924 (ptm-80) outliers start: 139 outliers final: 80 residues processed: 265 average time/residue: 0.3607 time to fit residues: 147.1172 Evaluate side-chains 214 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 124 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 163 optimal weight: 0.0170 chunk 243 optimal weight: 30.0000 chunk 258 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 231 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN D 104 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22527 Z= 0.169 Angle : 0.605 8.776 30879 Z= 0.310 Chirality : 0.042 0.191 3581 Planarity : 0.004 0.053 3748 Dihedral : 12.498 129.236 3750 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.64 % Favored : 92.10 % Rotamer: Outliers : 3.82 % Allowed : 31.87 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.66 (0.16), residues: 2650 helix: 0.30 (0.17), residues: 950 sheet: -1.07 (0.35), residues: 229 loop : -2.15 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 182 HIS 0.006 0.001 HIS E 554 PHE 0.017 0.001 PHE A 102 TYR 0.016 0.001 TYR A 237 ARG 0.007 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 142 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7846 (tpp) cc_final: 0.7587 (tpp) REVERT: A 161 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7668 (t0) REVERT: A 258 ASP cc_start: 0.8711 (m-30) cc_final: 0.8505 (t0) REVERT: A 380 MET cc_start: 0.7819 (mmm) cc_final: 0.7611 (mmt) REVERT: A 924 MET cc_start: 0.8849 (mmm) cc_final: 0.8339 (mtt) REVERT: B 75 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8324 (ttp80) REVERT: B 77 GLU cc_start: 0.8391 (tp30) cc_final: 0.7967 (tp30) REVERT: C 19 GLN cc_start: 0.8584 (mp10) cc_final: 0.7880 (mp10) REVERT: C 38 ASP cc_start: 0.8892 (t0) cc_final: 0.8570 (t0) REVERT: F 9 ASN cc_start: 0.8125 (t0) cc_final: 0.7868 (m-40) REVERT: F 68 MET cc_start: 0.8088 (mtm) cc_final: 0.7020 (mmt) REVERT: F 185 TYR cc_start: 0.8319 (p90) cc_final: 0.8017 (p90) REVERT: F 576 MET cc_start: -0.0018 (mmt) cc_final: -0.2404 (mtt) REVERT: E 233 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7269 (mmm) REVERT: E 274 MET cc_start: 0.8297 (mmm) cc_final: 0.7489 (mmp) REVERT: E 429 MET cc_start: 0.4353 (ptm) cc_final: 0.4142 (ppp) REVERT: E 554 HIS cc_start: 0.2837 (OUTLIER) cc_final: 0.1699 (t-170) outliers start: 86 outliers final: 50 residues processed: 217 average time/residue: 0.3821 time to fit residues: 127.2030 Evaluate side-chains 178 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 381 HIS A 698 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22527 Z= 0.398 Angle : 0.702 9.249 30879 Z= 0.362 Chirality : 0.045 0.252 3581 Planarity : 0.005 0.051 3748 Dihedral : 12.565 131.820 3748 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.27 % Favored : 90.43 % Rotamer: Outliers : 5.05 % Allowed : 31.34 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.91 (0.16), residues: 2650 helix: -0.04 (0.17), residues: 950 sheet: -1.31 (0.34), residues: 239 loop : -2.18 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 916 HIS 0.007 0.001 HIS F 39 PHE 0.021 0.002 PHE A 741 TYR 0.022 0.002 TYR A 788 ARG 0.007 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 129 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.9155 (tp40) cc_final: 0.8917 (tp-100) REVERT: A 40 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8861 (p0) REVERT: A 63 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8682 (t0) REVERT: A 110 MET cc_start: 0.7979 (tpp) cc_final: 0.7710 (mmm) REVERT: A 161 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 668 MET cc_start: 0.9053 (ttp) cc_final: 0.8627 (ttt) REVERT: A 924 MET cc_start: 0.8866 (mmm) cc_final: 0.8512 (mtt) REVERT: B 78 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8940 (t0) REVERT: C 19 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: C 38 ASP cc_start: 0.9042 (t0) cc_final: 0.8787 (t0) REVERT: D 75 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7437 (tpt-90) REVERT: D 128 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6569 (tp) REVERT: F 9 ASN cc_start: 0.8438 (t0) cc_final: 0.8169 (m-40) REVERT: F 68 MET cc_start: 0.8388 (mtm) cc_final: 0.7325 (mmt) REVERT: F 185 TYR cc_start: 0.8437 (p90) cc_final: 0.8134 (p90) REVERT: F 289 SER cc_start: 0.4752 (OUTLIER) cc_final: 0.4441 (p) REVERT: F 422 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.5389 (m-10) REVERT: F 512 ILE cc_start: 0.1013 (OUTLIER) cc_final: 0.0465 (mt) REVERT: F 576 MET cc_start: -0.0236 (mmt) cc_final: -0.2547 (mtt) REVERT: E 233 MET cc_start: 0.8270 (mpm) cc_final: 0.7579 (tpp) REVERT: E 274 MET cc_start: 0.8384 (mmm) cc_final: 0.7827 (mmm) REVERT: E 475 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4633 (p90) REVERT: E 554 HIS cc_start: 0.3027 (OUTLIER) cc_final: 0.1302 (t-170) outliers start: 114 outliers final: 74 residues processed: 233 average time/residue: 0.3356 time to fit residues: 123.6960 Evaluate side-chains 210 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 125 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 151 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 chunk 258 optimal weight: 9.9990 chunk 214 optimal weight: 50.0000 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 312 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN F 459 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22527 Z= 0.173 Angle : 0.592 8.057 30879 Z= 0.302 Chirality : 0.041 0.189 3581 Planarity : 0.004 0.050 3748 Dihedral : 12.304 114.073 3746 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.75 % Favored : 91.98 % Rotamer: Outliers : 4.08 % Allowed : 32.22 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.55 (0.16), residues: 2650 helix: 0.32 (0.17), residues: 945 sheet: -0.94 (0.35), residues: 239 loop : -2.04 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 182 HIS 0.010 0.001 HIS E 554 PHE 0.016 0.001 PHE E 422 TYR 0.017 0.001 TYR A 237 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 133 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7874 (tpp) cc_final: 0.7610 (mmm) REVERT: A 161 ASP cc_start: 0.8097 (m-30) cc_final: 0.7793 (t0) REVERT: A 258 ASP cc_start: 0.8529 (t0) cc_final: 0.8289 (t0) REVERT: A 924 MET cc_start: 0.8856 (mmm) cc_final: 0.8333 (mtt) REVERT: B 77 GLU cc_start: 0.8376 (tp30) cc_final: 0.8034 (tp30) REVERT: C 38 ASP cc_start: 0.8941 (t0) cc_final: 0.8645 (t0) REVERT: D 75 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7478 (tpt-90) REVERT: F 9 ASN cc_start: 0.8292 (t0) cc_final: 0.8041 (m-40) REVERT: F 68 MET cc_start: 0.8225 (mtm) cc_final: 0.7104 (mmt) REVERT: F 185 TYR cc_start: 0.8410 (p90) cc_final: 0.8105 (p90) REVERT: F 194 GLN cc_start: 0.7352 (tp40) cc_final: 0.7058 (tm-30) REVERT: F 289 SER cc_start: 0.4518 (OUTLIER) cc_final: 0.4231 (p) REVERT: F 422 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5294 (m-10) REVERT: F 550 THR cc_start: 0.0336 (OUTLIER) cc_final: -0.0192 (t) REVERT: F 576 MET cc_start: -0.0198 (mmt) cc_final: -0.2546 (mtt) REVERT: E 233 MET cc_start: 0.8235 (mpm) cc_final: 0.7468 (mmm) REVERT: E 274 MET cc_start: 0.8413 (mmm) cc_final: 0.7376 (mmp) REVERT: E 475 PHE cc_start: 0.5189 (OUTLIER) cc_final: 0.4596 (p90) REVERT: E 554 HIS cc_start: 0.2350 (OUTLIER) cc_final: 0.1359 (t-170) outliers start: 92 outliers final: 61 residues processed: 217 average time/residue: 0.3483 time to fit residues: 118.1667 Evaluate side-chains 193 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 127 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 144 optimal weight: 0.0980 chunk 257 optimal weight: 8.9990 chunk 161 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 168 ASN D 43 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22527 Z= 0.380 Angle : 0.682 9.290 30879 Z= 0.351 Chirality : 0.045 0.257 3581 Planarity : 0.005 0.049 3748 Dihedral : 12.349 100.458 3743 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.42 % Favored : 90.39 % Rotamer: Outliers : 4.52 % Allowed : 31.61 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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 (0.16), residues: 2650 helix: 0.02 (0.17), residues: 949 sheet: -1.24 (0.32), residues: 261 loop : -2.15 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 916 HIS 0.009 0.001 HIS E 290 PHE 0.021 0.002 PHE F 373 TYR 0.021 0.002 TYR A 887 ARG 0.010 0.001 ARG F 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 122 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.9298 (OUTLIER) cc_final: 0.8749 (t70) REVERT: A 110 MET cc_start: 0.7893 (tpp) cc_final: 0.7599 (mmm) REVERT: A 161 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 258 ASP cc_start: 0.8644 (t0) cc_final: 0.8327 (t0) REVERT: A 668 MET cc_start: 0.9040 (ttp) cc_final: 0.8632 (ttt) REVERT: A 924 MET cc_start: 0.8861 (mmm) cc_final: 0.8503 (mtp) REVERT: B 57 ARG cc_start: 0.7219 (mpt180) cc_final: 0.6770 (mpt180) REVERT: C 38 ASP cc_start: 0.9017 (t0) cc_final: 0.8763 (t0) REVERT: D 128 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6556 (tp) REVERT: F 9 ASN cc_start: 0.8481 (t0) cc_final: 0.8209 (m-40) REVERT: F 68 MET cc_start: 0.8455 (mtm) cc_final: 0.7425 (mmt) REVERT: F 185 TYR cc_start: 0.8440 (p90) cc_final: 0.8138 (p90) REVERT: F 194 GLN cc_start: 0.7600 (tp40) cc_final: 0.7297 (tm-30) REVERT: F 289 SER cc_start: 0.4737 (OUTLIER) cc_final: 0.4420 (p) REVERT: F 422 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5350 (m-10) REVERT: F 436 MET cc_start: 0.5950 (mpt) cc_final: 0.5649 (mpt) REVERT: F 550 THR cc_start: 0.0376 (OUTLIER) cc_final: -0.0083 (t) REVERT: F 576 MET cc_start: -0.0129 (mmt) cc_final: -0.2555 (mtt) REVERT: E 185 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7508 (t80) REVERT: E 274 MET cc_start: 0.8460 (mmm) cc_final: 0.8142 (mmp) REVERT: E 475 PHE cc_start: 0.5121 (OUTLIER) cc_final: 0.4573 (p90) REVERT: E 554 HIS cc_start: 0.3108 (OUTLIER) cc_final: 0.1410 (t-170) REVERT: G 32 TYR cc_start: 0.7051 (m-80) cc_final: 0.6817 (m-80) outliers start: 102 outliers final: 76 residues processed: 215 average time/residue: 0.3352 time to fit residues: 113.1175 Evaluate side-chains 204 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 119 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 163 optimal weight: 0.3980 chunk 175 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22527 Z= 0.161 Angle : 0.586 8.677 30879 Z= 0.298 Chirality : 0.041 0.244 3581 Planarity : 0.004 0.050 3748 Dihedral : 12.042 73.562 3743 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.83 % Favored : 92.02 % Rotamer: Outliers : 3.34 % Allowed : 32.48 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.57 (0.16), residues: 2650 helix: 0.31 (0.17), residues: 950 sheet: -1.28 (0.35), residues: 224 loop : -2.00 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 182 HIS 0.006 0.001 HIS E 554 PHE 0.019 0.001 PHE A 753 TYR 0.016 0.001 TYR A 237 ARG 0.006 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 128 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7247 (tptp) cc_final: 0.6842 (tptp) REVERT: A 110 MET cc_start: 0.7905 (tpp) cc_final: 0.7604 (mmm) REVERT: A 161 ASP cc_start: 0.8127 (m-30) cc_final: 0.7856 (t0) REVERT: A 258 ASP cc_start: 0.8560 (t0) cc_final: 0.8210 (t0) REVERT: A 396 PHE cc_start: 0.8368 (t80) cc_final: 0.8159 (t80) REVERT: A 668 MET cc_start: 0.8964 (ttp) cc_final: 0.8474 (ttt) REVERT: A 924 MET cc_start: 0.8802 (mmm) cc_final: 0.8337 (mtp) REVERT: B 77 GLU cc_start: 0.8345 (tp30) cc_final: 0.8023 (tp30) REVERT: B 129 MET cc_start: 0.8976 (mtm) cc_final: 0.8775 (mtt) REVERT: C 38 ASP cc_start: 0.8919 (t0) cc_final: 0.8615 (t0) REVERT: F 9 ASN cc_start: 0.8323 (t0) cc_final: 0.8053 (m-40) REVERT: F 68 MET cc_start: 0.8253 (mtm) cc_final: 0.7172 (mmt) REVERT: F 95 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7298 (m110) REVERT: F 185 TYR cc_start: 0.8411 (p90) cc_final: 0.8109 (p90) REVERT: F 194 GLN cc_start: 0.7475 (tp40) cc_final: 0.7142 (tm-30) REVERT: F 289 SER cc_start: 0.4572 (OUTLIER) cc_final: 0.4282 (p) REVERT: F 422 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5337 (m-10) REVERT: F 436 MET cc_start: 0.5783 (mpt) cc_final: 0.5476 (mpt) REVERT: F 550 THR cc_start: 0.0427 (OUTLIER) cc_final: -0.0046 (t) REVERT: F 576 MET cc_start: -0.0318 (mmt) cc_final: -0.2706 (mtt) REVERT: E 185 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7417 (t80) REVERT: E 233 MET cc_start: 0.8232 (mpm) cc_final: 0.7510 (mmm) REVERT: E 274 MET cc_start: 0.8477 (mmm) cc_final: 0.8181 (mmp) REVERT: E 475 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4532 (p90) REVERT: E 554 HIS cc_start: 0.2960 (OUTLIER) cc_final: 0.1531 (t-170) outliers start: 75 outliers final: 57 residues processed: 195 average time/residue: 0.3501 time to fit residues: 107.4183 Evaluate side-chains 188 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 124 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.0040 chunk 246 optimal weight: 40.0000 chunk 224 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 144 optimal weight: 0.0000 chunk 104 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 238 optimal weight: 0.5980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22527 Z= 0.182 Angle : 0.586 9.099 30879 Z= 0.298 Chirality : 0.041 0.250 3581 Planarity : 0.004 0.048 3748 Dihedral : 11.899 73.571 3743 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.40 % Favored : 91.45 % Rotamer: Outliers : 3.38 % Allowed : 32.27 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.51 (0.16), residues: 2650 helix: 0.33 (0.17), residues: 952 sheet: -1.07 (0.34), residues: 236 loop : -1.97 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.009 0.001 HIS E 554 PHE 0.020 0.001 PHE F 373 TYR 0.014 0.001 TYR G 89 ARG 0.007 0.000 ARG E 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 128 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7219 (tptp) cc_final: 0.6823 (tptp) REVERT: A 110 MET cc_start: 0.7900 (tpp) cc_final: 0.7587 (mmm) REVERT: A 161 ASP cc_start: 0.8107 (m-30) cc_final: 0.7849 (t0) REVERT: A 258 ASP cc_start: 0.8575 (t0) cc_final: 0.8206 (t0) REVERT: A 629 MET cc_start: 0.8117 (mmt) cc_final: 0.7683 (mmt) REVERT: A 668 MET cc_start: 0.8977 (ttp) cc_final: 0.8488 (ttt) REVERT: A 924 MET cc_start: 0.8816 (mmm) cc_final: 0.8379 (mtp) REVERT: B 77 GLU cc_start: 0.8329 (tp30) cc_final: 0.7833 (tp30) REVERT: C 38 ASP cc_start: 0.8947 (t0) cc_final: 0.8651 (t0) REVERT: D 44 VAL cc_start: 0.8465 (m) cc_final: 0.8082 (m) REVERT: F 9 ASN cc_start: 0.8320 (t0) cc_final: 0.8051 (m-40) REVERT: F 68 MET cc_start: 0.8263 (mtm) cc_final: 0.7139 (mmt) REVERT: F 185 TYR cc_start: 0.8421 (p90) cc_final: 0.8116 (p90) REVERT: F 194 GLN cc_start: 0.7455 (tp40) cc_final: 0.7109 (tm-30) REVERT: F 289 SER cc_start: 0.4603 (OUTLIER) cc_final: 0.4310 (p) REVERT: F 422 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5347 (m-10) REVERT: F 436 MET cc_start: 0.5725 (mpt) cc_final: 0.5393 (mpt) REVERT: F 550 THR cc_start: 0.0356 (OUTLIER) cc_final: -0.0152 (t) REVERT: F 576 MET cc_start: -0.0305 (mmt) cc_final: -0.2775 (mtt) REVERT: E 185 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7415 (t80) REVERT: E 233 MET cc_start: 0.8264 (mpm) cc_final: 0.7528 (mmm) REVERT: E 274 MET cc_start: 0.8447 (mmm) cc_final: 0.8140 (mmp) REVERT: E 475 PHE cc_start: 0.5115 (OUTLIER) cc_final: 0.4508 (p90) REVERT: E 554 HIS cc_start: 0.3188 (OUTLIER) cc_final: 0.1818 (p-80) outliers start: 76 outliers final: 62 residues processed: 198 average time/residue: 0.3330 time to fit residues: 104.2266 Evaluate side-chains 194 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 126 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 459 ASN Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 0.0370 chunk 253 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 22527 Z= 0.289 Angle : 0.826 59.175 30879 Z= 0.493 Chirality : 0.043 0.521 3581 Planarity : 0.006 0.207 3748 Dihedral : 11.904 73.571 3743 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.25 % Favored : 91.60 % Rotamer: Outliers : 3.25 % Allowed : 32.31 % Favored : 64.44 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.93 % 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: -1.50 (0.16), residues: 2650 helix: 0.34 (0.17), residues: 952 sheet: -1.07 (0.34), residues: 236 loop : -1.98 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.128 0.002 HIS E 554 PHE 0.019 0.001 PHE F 373 TYR 0.029 0.001 TYR E 457 ARG 0.005 0.000 ARG F 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 126 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7220 (tptp) cc_final: 0.6823 (tptp) REVERT: A 63 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.8992 (t70) REVERT: A 110 MET cc_start: 0.7901 (tpp) cc_final: 0.7587 (mmm) REVERT: A 161 ASP cc_start: 0.8109 (m-30) cc_final: 0.7849 (t0) REVERT: A 258 ASP cc_start: 0.8573 (t0) cc_final: 0.8212 (t0) REVERT: A 380 MET cc_start: 0.8057 (tpt) cc_final: 0.7794 (tpp) REVERT: A 629 MET cc_start: 0.8119 (mmt) cc_final: 0.7688 (mmt) REVERT: A 668 MET cc_start: 0.8978 (ttp) cc_final: 0.8490 (ttt) REVERT: A 924 MET cc_start: 0.8815 (mmm) cc_final: 0.8374 (mtp) REVERT: B 77 GLU cc_start: 0.8320 (tp30) cc_final: 0.7836 (tp30) REVERT: C 38 ASP cc_start: 0.8946 (t0) cc_final: 0.8651 (t0) REVERT: F 9 ASN cc_start: 0.8320 (t0) cc_final: 0.8051 (m-40) REVERT: F 68 MET cc_start: 0.8262 (mtm) cc_final: 0.7139 (mmt) REVERT: F 185 TYR cc_start: 0.8420 (p90) cc_final: 0.8116 (p90) REVERT: F 194 GLN cc_start: 0.7454 (tp40) cc_final: 0.7109 (tm-30) REVERT: F 289 SER cc_start: 0.4602 (OUTLIER) cc_final: 0.4310 (p) REVERT: F 422 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5350 (m-10) REVERT: F 436 MET cc_start: 0.5724 (mpt) cc_final: 0.5318 (mpt) REVERT: F 550 THR cc_start: 0.0356 (OUTLIER) cc_final: -0.0152 (t) REVERT: F 576 MET cc_start: -0.0293 (mmt) cc_final: -0.2786 (mtt) REVERT: E 185 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7415 (t80) REVERT: E 233 MET cc_start: 0.8266 (mpm) cc_final: 0.7528 (mmm) REVERT: E 274 MET cc_start: 0.8447 (mmm) cc_final: 0.8138 (mmp) REVERT: E 475 PHE cc_start: 0.5104 (OUTLIER) cc_final: 0.4508 (p90) REVERT: E 554 HIS cc_start: 0.3497 (OUTLIER) cc_final: 0.2269 (t70) outliers start: 73 outliers final: 63 residues processed: 193 average time/residue: 0.3302 time to fit residues: 101.1285 Evaluate side-chains 195 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 125 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 318 CYS Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 554 HIS Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 195 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.120410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069816 restraints weight = 113882.833| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 6.28 r_work: 0.2970 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 22527 Z= 0.289 Angle : 0.826 59.175 30879 Z= 0.493 Chirality : 0.043 0.521 3581 Planarity : 0.006 0.207 3748 Dihedral : 11.904 73.571 3743 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.25 % Favored : 91.60 % Rotamer: Outliers : 3.12 % Allowed : 32.40 % Favored : 64.49 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.93 % 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: -1.50 (0.16), residues: 2650 helix: 0.34 (0.17), residues: 952 sheet: -1.07 (0.34), residues: 236 loop : -1.98 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.128 0.002 HIS E 554 PHE 0.019 0.001 PHE F 373 TYR 0.029 0.001 TYR E 457 ARG 0.005 0.000 ARG F 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6238.36 seconds wall clock time: 113 minutes 30.30 seconds (6810.30 seconds total)