Starting phenix.real_space_refine on Mon Mar 18 19:42:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwg_34312/03_2024/8gwg_34312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwg_34312/03_2024/8gwg_34312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwg_34312/03_2024/8gwg_34312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwg_34312/03_2024/8gwg_34312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwg_34312/03_2024/8gwg_34312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwg_34312/03_2024/8gwg_34312_updated.pdb" } resolution = 3.37 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= -0.001 sd= 0.029 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.19, per 1000 atoms: 0.74 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: 8.79 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: 10.24 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: 7.41 Time building geometry restraints manager: 9.69 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: 3.890 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: 19.190 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 75.610 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.120 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1795 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 463 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 347 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: -0.2328 (OUTLIER) cc_final: -0.2780 (t) REVERT: A 520 SER cc_start: -0.0143 (OUTLIER) cc_final: -0.0412 (t) REVERT: A 629 MET cc_start: 0.0013 (mmm) cc_final: -0.0275 (pmm) REVERT: A 835 SER cc_start: 0.1783 (OUTLIER) cc_final: 0.1238 (m) REVERT: D 62 MET cc_start: 0.1578 (tmm) cc_final: 0.1267 (ppp) REVERT: D 179 ASN cc_start: 0.3873 (OUTLIER) cc_final: 0.2321 (m-40) REVERT: D 187 THR cc_start: 0.4711 (OUTLIER) cc_final: 0.3903 (p) REVERT: D 189 LEU cc_start: 0.6175 (mp) cc_final: 0.5881 (mt) REVERT: F 43 LEU cc_start: 0.7239 (mt) cc_final: 0.6989 (tt) REVERT: F 247 VAL cc_start: 0.4141 (t) cc_final: 0.2619 (t) REVERT: F 248 ARG cc_start: 0.5941 (tmm160) cc_final: 0.5060 (ptt-90) REVERT: F 274 MET cc_start: 0.2108 (ppp) cc_final: 0.1751 (pmm) REVERT: F 305 VAL cc_start: 0.7848 (t) cc_final: 0.7422 (t) REVERT: F 453 SER cc_start: -0.2824 (OUTLIER) cc_final: -0.3137 (m) REVERT: F 539 SER cc_start: 0.3734 (m) cc_final: 0.3234 (p) REVERT: F 561 PHE cc_start: 0.2848 (p90) cc_final: 0.2497 (m-10) REVERT: E 315 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6448 (p0) REVERT: E 430 LYS cc_start: 0.5031 (tmtm) cc_final: 0.4704 (mmtt) outliers start: 116 outliers final: 22 residues processed: 448 average time/residue: 0.3378 time to fit residues: 231.4975 Evaluate side-chains 224 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 84 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 198 ASN A 381 HIS A 414 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 492 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 816 HIS B 65 GLN B 100 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 492 GLN F 516 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 ASN ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3372 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 22527 Z= 0.415 Angle : 1.014 16.861 30879 Z= 0.518 Chirality : 0.054 0.323 3581 Planarity : 0.008 0.084 3748 Dihedral : 13.477 149.928 3779 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.08 % Favored : 90.58 % Rotamer: Outliers : 7.68 % Allowed : 29.94 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.15), residues: 2650 helix: -0.90 (0.16), residues: 945 sheet: -1.81 (0.34), residues: 212 loop : -2.59 (0.14), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP A 916 HIS 0.021 0.003 HIS A 642 PHE 0.051 0.004 PHE A 859 TYR 0.032 0.003 TYR A 516 ARG 0.024 0.001 ARG A 569 *********************** 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 432 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 260 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.5142 (OUTLIER) cc_final: 0.2861 (mtm-85) REVERT: A 152 CYS cc_start: 0.4481 (p) cc_final: 0.4213 (m) REVERT: A 349 ARG cc_start: 0.1563 (mmt180) cc_final: 0.0833 (ttp80) REVERT: A 426 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5348 (mtpt) REVERT: A 579 ILE cc_start: 0.7003 (mt) cc_final: 0.6538 (mt) REVERT: A 629 MET cc_start: 0.2140 (mmm) cc_final: 0.1463 (pmm) REVERT: A 782 PHE cc_start: 0.4729 (m-80) cc_final: 0.4202 (m-80) REVERT: A 788 TYR cc_start: 0.0617 (OUTLIER) cc_final: 0.0248 (p90) REVERT: A 813 CYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7265 (m) REVERT: A 881 PHE cc_start: 0.3474 (t80) cc_final: 0.3141 (t80) REVERT: A 924 MET cc_start: 0.5042 (OUTLIER) cc_final: 0.4658 (mtt) REVERT: B 61 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5953 (mmtt) REVERT: B 103 LEU cc_start: 0.3915 (OUTLIER) cc_final: 0.3647 (mm) REVERT: D 90 MET cc_start: 0.3569 (mtp) cc_final: 0.3144 (mtp) REVERT: D 158 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6205 (pp30) REVERT: D 160 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.6762 (t) REVERT: D 161 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: D 187 THR cc_start: 0.6243 (p) cc_final: 0.5752 (p) REVERT: F 185 TYR cc_start: 0.8260 (p90) cc_final: 0.7968 (p90) REVERT: F 248 ARG cc_start: 0.5930 (tmm160) cc_final: 0.5671 (tpt170) REVERT: F 274 MET cc_start: 0.3060 (ppp) cc_final: 0.2694 (pmm) REVERT: F 539 SER cc_start: 0.4145 (m) cc_final: 0.3785 (p) REVERT: F 561 PHE cc_start: 0.2937 (p90) cc_final: 0.2611 (m-10) REVERT: E 378 MET cc_start: 0.6765 (ppp) cc_final: 0.6290 (tmm) REVERT: E 430 LYS cc_start: 0.4843 (tmtm) cc_final: 0.4523 (mmtt) REVERT: G 23 CYS cc_start: 0.1361 (OUTLIER) cc_final: 0.0810 (m) REVERT: G 35 THR cc_start: 0.1131 (OUTLIER) cc_final: 0.0832 (m) outliers start: 172 outliers final: 54 residues processed: 406 average time/residue: 0.3411 time to fit residues: 214.1448 Evaluate side-chains 261 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 195 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 694 PHE Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 92 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 262 optimal weight: 0.4980 chunk 216 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 177 ASN A 209 ASN A 292 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 176 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 98 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3451 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22527 Z= 0.205 Angle : 0.711 9.836 30879 Z= 0.359 Chirality : 0.043 0.191 3581 Planarity : 0.005 0.085 3748 Dihedral : 12.874 146.441 3743 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.83 % Favored : 91.91 % Rotamer: Outliers : 4.26 % Allowed : 32.48 % Favored : 63.26 % Cbeta Deviations : 0.00 % 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: -2.29 (0.15), residues: 2650 helix: -0.37 (0.17), residues: 936 sheet: -1.35 (0.35), residues: 200 loop : -2.40 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 916 HIS 0.005 0.001 HIS A 725 PHE 0.019 0.002 PHE A 753 TYR 0.030 0.002 TYR A 455 ARG 0.006 0.001 ARG E 15 *********************** 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 302 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 208 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.6971 (tmmt) cc_final: 0.6719 (tppt) REVERT: A 127 LEU cc_start: 0.0358 (OUTLIER) cc_final: -0.0201 (tt) REVERT: A 196 MET cc_start: -0.0809 (tpp) cc_final: -0.2023 (ptp) REVERT: A 468 GLN cc_start: 0.3336 (OUTLIER) cc_final: 0.2479 (tt0) REVERT: A 515 TYR cc_start: 0.1062 (m-80) cc_final: 0.0472 (m-80) REVERT: A 519 MET cc_start: 0.0086 (OUTLIER) cc_final: -0.0166 (mtp) REVERT: A 782 PHE cc_start: 0.4617 (m-80) cc_final: 0.4026 (m-80) REVERT: F 156 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5368 (pm20) REVERT: F 164 HIS cc_start: 0.5454 (OUTLIER) cc_final: 0.5168 (t-90) REVERT: F 185 TYR cc_start: 0.8197 (p90) cc_final: 0.7875 (p90) REVERT: F 248 ARG cc_start: 0.5979 (tmm160) cc_final: 0.5507 (tpt170) REVERT: F 274 MET cc_start: 0.3136 (ppp) cc_final: 0.2607 (pmm) REVERT: F 539 SER cc_start: 0.4103 (m) cc_final: 0.3801 (p) REVERT: F 561 PHE cc_start: 0.3047 (p90) cc_final: 0.2690 (m-10) REVERT: E 359 THR cc_start: -0.3473 (OUTLIER) cc_final: -0.3757 (m) REVERT: E 430 LYS cc_start: 0.4933 (tttm) cc_final: 0.4731 (mmtt) REVERT: E 432 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3456 (mp) REVERT: E 575 ILE cc_start: -0.0727 (OUTLIER) cc_final: -0.1122 (tp) REVERT: G 35 THR cc_start: 0.1604 (OUTLIER) cc_final: 0.1363 (m) outliers start: 94 outliers final: 47 residues processed: 287 average time/residue: 0.3347 time to fit residues: 153.7755 Evaluate side-chains 239 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 183 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 177 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 713 ASN A 781 ASN ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4430 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 22527 Z= 0.371 Angle : 0.908 19.234 30879 Z= 0.463 Chirality : 0.051 0.345 3581 Planarity : 0.007 0.105 3748 Dihedral : 13.163 128.521 3742 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.42 % Favored : 90.28 % Rotamer: Outliers : 6.41 % Allowed : 31.91 % Favored : 61.68 % Cbeta Deviations : 0.00 % 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: -2.74 (0.15), residues: 2650 helix: -0.84 (0.16), residues: 923 sheet: -1.94 (0.34), residues: 214 loop : -2.54 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 216 HIS 0.010 0.002 HIS A 725 PHE 0.032 0.003 PHE A 694 TYR 0.057 0.003 TYR G 87 ARG 0.019 0.001 ARG A 467 *********************** 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 369 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 226 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.6959 (tmmt) cc_final: 0.6688 (tppt) REVERT: A 196 MET cc_start: -0.0434 (tpp) cc_final: -0.2017 (ptt) REVERT: A 270 LEU cc_start: 0.5635 (pt) cc_final: 0.5184 (mp) REVERT: A 408 GLN cc_start: 0.0772 (OUTLIER) cc_final: 0.0295 (mp10) REVERT: A 549 SER cc_start: 0.5997 (p) cc_final: 0.5770 (p) REVERT: A 788 TYR cc_start: 0.1020 (OUTLIER) cc_final: 0.0575 (p90) REVERT: A 888 ILE cc_start: 0.8131 (mt) cc_final: 0.7889 (mt) REVERT: D 128 LEU cc_start: 0.1206 (OUTLIER) cc_final: 0.0201 (tp) REVERT: D 182 TRP cc_start: 0.2347 (OUTLIER) cc_final: 0.2044 (p90) REVERT: F 120 TYR cc_start: -0.2478 (OUTLIER) cc_final: -0.2780 (t80) REVERT: F 156 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5306 (pm20) REVERT: F 164 HIS cc_start: 0.5210 (OUTLIER) cc_final: 0.4961 (t-90) REVERT: F 241 VAL cc_start: 0.2358 (OUTLIER) cc_final: 0.2113 (t) REVERT: F 248 ARG cc_start: 0.5958 (tmm160) cc_final: 0.5453 (tpt170) REVERT: F 561 PHE cc_start: 0.2993 (p90) cc_final: 0.2742 (m-10) REVERT: E 68 MET cc_start: 0.7458 (mmt) cc_final: 0.6920 (pmm) REVERT: E 131 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5184 (ttmm) REVERT: E 378 MET cc_start: 0.7141 (ppp) cc_final: 0.6640 (ppp) REVERT: E 432 ILE cc_start: 0.3885 (OUTLIER) cc_final: 0.3670 (mp) REVERT: G 23 CYS cc_start: 0.1379 (OUTLIER) cc_final: 0.0827 (m) REVERT: G 35 THR cc_start: 0.2199 (OUTLIER) cc_final: 0.1954 (m) REVERT: G 86 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.4959 (mttt) outliers start: 143 outliers final: 66 residues processed: 345 average time/residue: 0.3242 time to fit residues: 175.5542 Evaluate side-chains 263 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 184 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 0.0070 chunk 146 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 106 optimal weight: 0.0370 chunk 220 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 231 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 overall best weight: 1.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 HIS B 69 GLN B 100 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 moved from start: 0.9511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 22527 Z= 0.326 Angle : 0.829 17.915 30879 Z= 0.421 Chirality : 0.047 0.291 3581 Planarity : 0.006 0.078 3748 Dihedral : 13.069 130.558 3740 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.21 % Favored : 91.57 % Rotamer: Outliers : 5.71 % Allowed : 32.27 % Favored : 62.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.15), residues: 2650 helix: -0.67 (0.16), residues: 922 sheet: -2.07 (0.34), residues: 204 loop : -2.43 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 617 HIS 0.019 0.002 HIS A 613 PHE 0.028 0.003 PHE A 571 TYR 0.037 0.002 TYR A 237 ARG 0.010 0.001 ARG G 39 *********************** 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 343 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 216 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7019 (tmmt) cc_final: 0.6723 (tppt) REVERT: A 103 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7352 (mtpp) REVERT: A 196 MET cc_start: -0.0157 (tpp) cc_final: -0.0842 (ptt) REVERT: A 246 THR cc_start: 0.3394 (m) cc_final: 0.2054 (p) REVERT: A 534 ASN cc_start: 0.1674 (OUTLIER) cc_final: 0.1149 (m-40) REVERT: A 575 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 615 MET cc_start: 0.5944 (ptt) cc_final: 0.5390 (tmm) REVERT: A 666 MET cc_start: 0.3357 (ppp) cc_final: 0.2934 (ptp) REVERT: A 668 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.3724 (tpt) REVERT: A 725 HIS cc_start: 0.5289 (OUTLIER) cc_final: 0.4647 (m-70) REVERT: A 764 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7833 (m) REVERT: A 788 TYR cc_start: 0.1261 (OUTLIER) cc_final: 0.0826 (p90) REVERT: A 898 HIS cc_start: 0.8282 (t-90) cc_final: 0.8035 (t70) REVERT: B 119 ILE cc_start: -0.0282 (OUTLIER) cc_final: -0.0660 (mm) REVERT: D 62 MET cc_start: 0.5761 (ppp) cc_final: 0.5343 (ppp) REVERT: D 158 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7177 (pp30) REVERT: F 25 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.4378 (mp) REVERT: F 120 TYR cc_start: -0.2268 (OUTLIER) cc_final: -0.2583 (t80) REVERT: F 156 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: F 241 VAL cc_start: 0.2077 (OUTLIER) cc_final: 0.1838 (t) REVERT: F 248 ARG cc_start: 0.5877 (tmm160) cc_final: 0.5374 (tpt170) REVERT: E 319 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6670 (pp20) REVERT: E 378 MET cc_start: 0.7098 (ppp) cc_final: 0.6668 (ppp) REVERT: E 432 ILE cc_start: 0.3855 (OUTLIER) cc_final: 0.3489 (mp) REVERT: G 23 CYS cc_start: 0.1373 (OUTLIER) cc_final: 0.0816 (m) REVERT: G 52 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.6127 (tmtt) REVERT: G 69 LEU cc_start: 0.4235 (tp) cc_final: 0.3912 (tp) outliers start: 127 outliers final: 63 residues processed: 321 average time/residue: 0.3302 time to fit residues: 165.4654 Evaluate side-chains 268 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 188 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 67 THR 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: 10.0000 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 258 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN F 388 ASN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5007 moved from start: 1.0332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22527 Z= 0.256 Angle : 0.742 11.875 30879 Z= 0.375 Chirality : 0.045 0.241 3581 Planarity : 0.005 0.082 3748 Dihedral : 12.977 139.880 3740 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.89 % Favored : 90.89 % Rotamer: Outliers : 5.36 % Allowed : 32.40 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.15), residues: 2650 helix: -0.50 (0.17), residues: 928 sheet: -2.10 (0.35), residues: 197 loop : -2.35 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 268 HIS 0.010 0.002 HIS F 395 PHE 0.045 0.002 PHE D 92 TYR 0.050 0.002 TYR A 346 ARG 0.007 0.001 ARG A 349 *********************** 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 322 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 203 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7386 (mtpp) REVERT: A 196 MET cc_start: 0.0173 (tpp) cc_final: -0.0416 (ptt) REVERT: A 270 LEU cc_start: 0.5404 (pt) cc_final: 0.4571 (mp) REVERT: A 615 MET cc_start: 0.6084 (ptt) cc_final: 0.5430 (tmm) REVERT: A 725 HIS cc_start: 0.5275 (OUTLIER) cc_final: 0.4500 (m-70) REVERT: A 726 ARG cc_start: 0.7316 (mmm160) cc_final: 0.6525 (mmp80) REVERT: A 729 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 756 MET cc_start: 0.7363 (tmm) cc_final: 0.6311 (ttp) REVERT: A 764 VAL cc_start: 0.8301 (t) cc_final: 0.8028 (m) REVERT: A 782 PHE cc_start: 0.6287 (m-80) cc_final: 0.5825 (t80) REVERT: A 807 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6514 (tptm) REVERT: B 119 ILE cc_start: -0.0140 (OUTLIER) cc_final: -0.0505 (mm) REVERT: D 158 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7266 (pp30) REVERT: F 120 TYR cc_start: -0.2021 (OUTLIER) cc_final: -0.2283 (t80) REVERT: F 156 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5426 (pm20) REVERT: F 241 VAL cc_start: 0.2040 (OUTLIER) cc_final: 0.1824 (t) REVERT: F 248 ARG cc_start: 0.6115 (tmm160) cc_final: 0.5650 (tpt170) REVERT: F 346 PHE cc_start: 0.2448 (OUTLIER) cc_final: 0.1097 (m-10) REVERT: E 25 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3699 (pp) REVERT: E 68 MET cc_start: 0.7030 (mmt) cc_final: 0.6600 (pmm) REVERT: E 319 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6597 (pp20) REVERT: E 378 MET cc_start: 0.7212 (ppp) cc_final: 0.6633 (ppp) REVERT: E 432 ILE cc_start: 0.3923 (OUTLIER) cc_final: 0.3650 (mp) REVERT: G 12 MET cc_start: 0.6976 (mpp) cc_final: 0.6665 (mmp) REVERT: G 23 CYS cc_start: 0.1614 (OUTLIER) cc_final: 0.1026 (m) outliers start: 119 outliers final: 74 residues processed: 302 average time/residue: 0.3265 time to fit residues: 157.1296 Evaluate side-chains 271 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 184 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 217 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN C 63 GLN F 388 ASN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 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: 0.5163 moved from start: 1.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22527 Z= 0.236 Angle : 0.735 15.535 30879 Z= 0.367 Chirality : 0.044 0.202 3581 Planarity : 0.005 0.073 3748 Dihedral : 12.953 143.563 3740 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.09 % Favored : 91.64 % Rotamer: Outliers : 4.43 % Allowed : 33.10 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -2.28 (0.15), residues: 2650 helix: -0.37 (0.17), residues: 919 sheet: -1.91 (0.35), residues: 198 loop : -2.28 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 509 HIS 0.017 0.001 HIS E 290 PHE 0.028 0.002 PHE A 101 TYR 0.029 0.002 TYR G 32 ARG 0.011 0.001 ARG A 721 *********************** 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 303 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 205 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.6790 (tmmt) cc_final: 0.6548 (tppt) REVERT: A 124 MET cc_start: -0.0991 (mtp) cc_final: -0.3432 (ttm) REVERT: A 129 TYR cc_start: 0.1315 (t80) cc_final: 0.1059 (t80) REVERT: A 201 ILE cc_start: 0.2394 (OUTLIER) cc_final: 0.1933 (mm) REVERT: A 211 ASP cc_start: 0.5397 (OUTLIER) cc_final: 0.4465 (p0) REVERT: A 355 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7396 (t-90) REVERT: A 668 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.4687 (tpt) REVERT: A 725 HIS cc_start: 0.6001 (OUTLIER) cc_final: 0.5435 (m-70) REVERT: A 756 MET cc_start: 0.7285 (tmm) cc_final: 0.6816 (ttt) REVERT: A 807 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7062 (tptm) REVERT: A 906 MET cc_start: 0.7777 (mmm) cc_final: 0.7353 (mpp) REVERT: D 135 TYR cc_start: 0.7029 (p90) cc_final: 0.6751 (p90) REVERT: D 158 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7069 (pp30) REVERT: F 120 TYR cc_start: -0.1677 (OUTLIER) cc_final: -0.1926 (t80) REVERT: F 156 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5743 (pm20) REVERT: F 248 ARG cc_start: 0.5883 (tmm160) cc_final: 0.5541 (tpt170) REVERT: F 346 PHE cc_start: 0.2273 (OUTLIER) cc_final: 0.1005 (m-10) REVERT: E 25 LEU cc_start: 0.4308 (OUTLIER) cc_final: 0.4008 (pp) REVERT: E 378 MET cc_start: 0.7244 (ppp) cc_final: 0.6884 (ppp) REVERT: G 23 CYS cc_start: 0.1857 (OUTLIER) cc_final: 0.1281 (m) outliers start: 98 outliers final: 74 residues processed: 284 average time/residue: 0.3183 time to fit residues: 142.8745 Evaluate side-chains 263 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 177 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 153 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 202 optimal weight: 8.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 100 ASN C 31 GLN C 36 HIS F 388 ASN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 moved from start: 1.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22527 Z= 0.182 Angle : 0.689 11.469 30879 Z= 0.343 Chirality : 0.043 0.203 3581 Planarity : 0.005 0.072 3748 Dihedral : 12.858 148.086 3740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.83 % Favored : 91.91 % Rotamer: Outliers : 4.08 % Allowed : 34.24 % Favored : 61.68 % 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: -2.15 (0.16), residues: 2650 helix: -0.19 (0.17), residues: 910 sheet: -1.97 (0.35), residues: 204 loop : -2.21 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 182 HIS 0.010 0.001 HIS F 33 PHE 0.038 0.002 PHE A 652 TYR 0.027 0.001 TYR A 346 ARG 0.004 0.000 ARG A 569 *********************** 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 283 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 193 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.6718 (tmmt) cc_final: 0.6495 (tppt) REVERT: A 124 MET cc_start: -0.1330 (mtp) cc_final: -0.3133 (ttm) REVERT: A 129 TYR cc_start: 0.1344 (t80) cc_final: 0.1031 (t80) REVERT: A 211 ASP cc_start: 0.5362 (p0) cc_final: 0.4759 (p0) REVERT: A 355 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: A 666 MET cc_start: 0.5012 (ppp) cc_final: 0.4769 (ptp) REVERT: A 725 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.5341 (m-70) REVERT: A 756 MET cc_start: 0.7255 (tmm) cc_final: 0.6866 (ttt) REVERT: A 764 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7941 (m) REVERT: A 807 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7207 (tptm) REVERT: A 906 MET cc_start: 0.7772 (mmm) cc_final: 0.7367 (mpp) REVERT: D 135 TYR cc_start: 0.7034 (p90) cc_final: 0.6783 (p90) REVERT: D 158 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7062 (pp30) REVERT: F 120 TYR cc_start: -0.1634 (OUTLIER) cc_final: -0.1861 (t80) REVERT: F 156 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5991 (pm20) REVERT: F 248 ARG cc_start: 0.6160 (tmm160) cc_final: 0.5720 (tpt170) REVERT: F 274 MET cc_start: 0.2750 (ppp) cc_final: 0.1829 (pmm) REVERT: F 346 PHE cc_start: 0.2246 (OUTLIER) cc_final: 0.0995 (m-10) REVERT: E 25 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.3980 (pp) REVERT: E 319 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6446 (pp20) REVERT: E 378 MET cc_start: 0.7275 (ppp) cc_final: 0.6957 (ppp) REVERT: G 23 CYS cc_start: 0.1817 (OUTLIER) cc_final: 0.1214 (m) outliers start: 90 outliers final: 69 residues processed: 267 average time/residue: 0.3305 time to fit residues: 140.1789 Evaluate side-chains 261 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 181 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.5980 chunk 246 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN F 51 ASN F 388 ASN F 470 GLN ** F 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 1.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22527 Z= 0.307 Angle : 0.837 17.412 30879 Z= 0.423 Chirality : 0.048 0.268 3581 Planarity : 0.006 0.079 3748 Dihedral : 13.076 145.856 3739 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.68 % Favored : 89.83 % Rotamer: Outliers : 4.92 % Allowed : 33.49 % Favored : 61.59 % 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: -2.45 (0.15), residues: 2650 helix: -0.57 (0.16), residues: 910 sheet: -2.09 (0.34), residues: 210 loop : -2.31 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 182 HIS 0.015 0.002 HIS A 613 PHE 0.034 0.003 PHE A 506 TYR 0.044 0.002 TYR A 149 ARG 0.018 0.001 ARG A 467 *********************** 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 323 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 214 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.6885 (tmmt) cc_final: 0.6565 (tppt) REVERT: A 293 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8135 (t) REVERT: A 316 LEU cc_start: 0.6595 (tp) cc_final: 0.5901 (mt) REVERT: A 368 PHE cc_start: 0.4809 (OUTLIER) cc_final: 0.4204 (t80) REVERT: A 668 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.5879 (tpt) REVERT: A 768 SER cc_start: 0.8216 (t) cc_final: 0.7919 (p) REVERT: A 807 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7798 (tmtt) REVERT: B 67 MET cc_start: 0.2853 (ptp) cc_final: 0.2605 (ptm) REVERT: C 34 GLN cc_start: 0.7474 (pp30) cc_final: 0.7214 (tp-100) REVERT: D 135 TYR cc_start: 0.7289 (p90) cc_final: 0.7040 (p90) REVERT: D 158 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6674 (pp30) REVERT: F 120 TYR cc_start: -0.1278 (OUTLIER) cc_final: -0.1529 (t80) REVERT: F 156 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5288 (pm20) REVERT: F 248 ARG cc_start: 0.6041 (tmm160) cc_final: 0.5616 (tpt170) REVERT: F 346 PHE cc_start: 0.2264 (OUTLIER) cc_final: 0.1017 (m-10) REVERT: F 508 LYS cc_start: 0.1933 (OUTLIER) cc_final: 0.1593 (mmtt) REVERT: E 25 LEU cc_start: 0.4851 (OUTLIER) cc_final: 0.4509 (pp) REVERT: E 319 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6473 (pp20) REVERT: E 378 MET cc_start: 0.7294 (ppp) cc_final: 0.6981 (ppp) REVERT: E 475 PHE cc_start: 0.4332 (OUTLIER) cc_final: 0.3709 (p90) REVERT: G 23 CYS cc_start: 0.2141 (OUTLIER) cc_final: 0.0744 (m) REVERT: G 66 TYR cc_start: 0.4969 (m-10) cc_final: 0.4470 (p90) outliers start: 109 outliers final: 69 residues processed: 306 average time/residue: 0.3510 time to fit residues: 165.8095 Evaluate side-chains 268 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 186 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 475 PHE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 0.0020 chunk 253 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 266 optimal weight: 0.0970 chunk 244 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 163 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 534 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 HIS ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 1.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22527 Z= 0.217 Angle : 0.723 12.135 30879 Z= 0.361 Chirality : 0.044 0.185 3581 Planarity : 0.005 0.071 3748 Dihedral : 13.007 154.158 3739 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.83 % Favored : 91.94 % Rotamer: Outliers : 3.86 % Allowed : 35.51 % Favored : 60.62 % 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: -2.18 (0.15), residues: 2650 helix: -0.28 (0.17), residues: 908 sheet: -1.82 (0.38), residues: 166 loop : -2.22 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 182 HIS 0.011 0.001 HIS C 36 PHE 0.030 0.002 PHE A 652 TYR 0.022 0.002 TYR A 80 ARG 0.007 0.001 ARG D 51 ********************** 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 290 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 205 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.6701 (tmmt) cc_final: 0.6486 (tppt) REVERT: A 217 TYR cc_start: 0.1640 (p90) cc_final: 0.0931 (t80) REVERT: A 266 ILE cc_start: 0.5249 (mm) cc_final: 0.4746 (tp) REVERT: A 633 MET cc_start: 0.7697 (mtt) cc_final: 0.7482 (ttp) REVERT: A 665 GLU cc_start: 0.7258 (pm20) cc_final: 0.7051 (pm20) REVERT: A 756 MET cc_start: 0.7566 (ttt) cc_final: 0.7331 (ttp) REVERT: A 768 SER cc_start: 0.7965 (t) cc_final: 0.7715 (p) REVERT: B 70 MET cc_start: 0.0940 (tpt) cc_final: 0.0557 (tpp) REVERT: B 169 LEU cc_start: 0.2863 (mp) cc_final: 0.2615 (mm) REVERT: D 75 ARG cc_start: 0.6820 (mmp80) cc_final: 0.6557 (tpt90) REVERT: D 135 TYR cc_start: 0.7231 (p90) cc_final: 0.7014 (p90) REVERT: D 158 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6579 (pp30) REVERT: F 120 TYR cc_start: -0.1094 (OUTLIER) cc_final: -0.1302 (t80) REVERT: F 156 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5478 (pm20) REVERT: F 248 ARG cc_start: 0.6021 (tmm160) cc_final: 0.5639 (tpt170) REVERT: F 274 MET cc_start: 0.2930 (ppp) cc_final: 0.1872 (pmm) REVERT: F 346 PHE cc_start: 0.2300 (OUTLIER) cc_final: 0.1045 (m-10) REVERT: E 25 LEU cc_start: 0.4907 (OUTLIER) cc_final: 0.4591 (pp) REVERT: E 319 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6519 (pp20) REVERT: E 378 MET cc_start: 0.7300 (ppp) cc_final: 0.6991 (ppp) REVERT: G 23 CYS cc_start: 0.2044 (OUTLIER) cc_final: 0.0662 (m) REVERT: G 66 TYR cc_start: 0.4771 (m-10) cc_final: 0.4394 (p90) outliers start: 85 outliers final: 67 residues processed: 277 average time/residue: 0.3488 time to fit residues: 151.7806 Evaluate side-chains 261 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 187 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 2.9990 chunk 225 optimal weight: 0.0070 chunk 64 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.183930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.147478 restraints weight = 112267.785| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 8.73 r_work: 0.4365 rms_B_bonded: 7.07 restraints_weight: 2.0000 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 1.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 22527 Z= 0.328 Angle : 0.851 59.186 30879 Z= 0.453 Chirality : 0.055 1.938 3581 Planarity : 0.005 0.071 3748 Dihedral : 13.003 154.182 3739 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.91 % Rotamer: Outliers : 3.78 % Allowed : 35.51 % Favored : 60.71 % Cbeta Deviations : 0.04 % 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: -2.18 (0.16), residues: 2650 helix: -0.25 (0.17), residues: 903 sheet: -1.80 (0.38), residues: 176 loop : -2.24 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP B 182 HIS 0.013 0.001 HIS F 464 PHE 0.024 0.002 PHE A 652 TYR 0.019 0.002 TYR A 80 ARG 0.063 0.001 ARG E 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6847.62 seconds wall clock time: 123 minutes 26.20 seconds (7406.20 seconds total)