Starting phenix.real_space_refine on Sat Mar 7 01:44:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x43_22039/03_2026/6x43_22039.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x43_22039/03_2026/6x43_22039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x43_22039/03_2026/6x43_22039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x43_22039/03_2026/6x43_22039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x43_22039/03_2026/6x43_22039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x43_22039/03_2026/6x43_22039.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 sd= 1.083 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 2 5.21 5 S 142 5.16 5 C 22295 2.51 5 N 6395 2.21 5 O 7106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36055 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8982 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10354 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1050 Classifications: {'DNA': 52} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "Q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23177 SG CYS J 70 25.219 93.395 101.684 1.00 98.41 S ATOM 23191 SG CYS J 72 24.700 96.981 100.720 1.00102.52 S ATOM 23299 SG CYS J 85 22.471 94.165 99.254 1.00104.97 S ATOM 23323 SG CYS J 88 26.183 94.049 98.464 1.00100.42 S ATOM 28999 SG CYS J 814 53.429 33.493 106.376 1.00 64.15 S ATOM 29564 SG CYS J 888 54.097 36.979 105.187 1.00 59.64 S ATOM 29636 SG CYS J 898 55.991 34.004 107.900 1.00 55.45 S Time building chain proxies: 6.85, per 1000 atoms: 0.19 Number of scatterers: 36055 At special positions: 0 Unit cell: (137.8, 193.7, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 142 16.00 P 113 15.00 Mg 2 11.99 O 7106 8.00 N 6395 7.00 C 22295 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 - 3.00 Amino acid : True - 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 55 sheets defined 37.9% alpha, 14.1% beta 49 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 48 through 63 removed outlier: 4.167A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 4.143A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 220 through 235 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 256 through 265 Proline residue: A 262 - end of helix removed outlier: 3.563A pdb=" N PHE A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.762A pdb=" N LEU A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.985A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.589A pdb=" N ALA A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 564 through 578 removed outlier: 3.596A pdb=" N LYS A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 4.336A pdb=" N PHE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 633 through 647 removed outlier: 3.992A pdb=" N VAL A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 688 through 702 removed outlier: 3.691A pdb=" N THR A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.770A pdb=" N GLN A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 746 removed outlier: 4.336A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 768 removed outlier: 3.981A pdb=" N ALA A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.552A pdb=" N ARG A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 833 removed outlier: 4.433A pdb=" N GLN A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 859 removed outlier: 3.784A pdb=" N ARG A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 918 through 922 removed outlier: 3.810A pdb=" N MET A 922 " --> pdb=" O PRO A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 936 Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 971 through 990 removed outlier: 3.790A pdb=" N GLU A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'A' and resid 1019 through 1032 Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.698A pdb=" N LYS A1072 " --> pdb=" O GLN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 3.711A pdb=" N ASN A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.585A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.981A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 88 removed outlier: 4.028A pdb=" N ASN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.596A pdb=" N ILE H 115 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.731A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.759A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 347 through 354 Processing helix chain 'I' and resid 359 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.572A pdb=" N ALA I 381 " --> pdb=" O THR I 377 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.652A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.806A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.676A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.930A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.839A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.075A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.972A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.689A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.613A pdb=" N LEU I 979 " --> pdb=" O ILE I 975 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.794A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.577A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.617A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.945A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.514A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.668A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.614A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.589A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.535A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.585A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.656A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.745A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.258A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.696A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.022A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.592A pdb=" N SER J 728 " --> pdb=" O MET J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.547A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.095A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.630A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.682A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.529A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.760A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.512A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.871A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.520A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 removed outlier: 3.701A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 removed outlier: 3.575A pdb=" N SER J1313 " --> pdb=" O ILE J1309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.592A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.505A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.541A pdb=" N VAL A 42 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 108 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU A 44 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 removed outlier: 5.424A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 194 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.066A pdb=" N VAL A 385 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN A 410 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 436 Processing sheet with id=AA7, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.569A pdb=" N MET A 510 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET A 496 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR A 508 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 498 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 506 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.456A pdb=" N GLU A 681 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 652 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLY A 709 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 654 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A 653 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP A 729 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 655 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 726 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 754 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 728 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG A 624 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP A 623 " --> pdb=" O ASP A 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 787 through 792 removed outlier: 6.055A pdb=" N LYS A 787 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 914 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 789 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR A 916 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 791 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 883 " --> pdb=" O TYR A 911 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN A 811 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 882 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1075 through 1078 Processing sheet with id=AB2, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.883A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB4, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.545A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB6, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.742A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 16 through 17 removed outlier: 6.271A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.638A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AC1, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AC2, first strand: chain 'H' and resid 108 through 109 Processing sheet with id=AC3, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.514A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.269A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC6, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.551A pdb=" N GLN I 148 " --> pdb=" O ARG I 454 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 154 through 160 removed outlier: 4.029A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.793A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.819A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.419A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 301 through 303 removed outlier: 7.192A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE I 310 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU I 308 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.440A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AD5, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AD6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.246A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.218A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.531A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 7.177A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.646A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.686A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AE4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE5, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.503A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE7, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE8, first strand: chain 'J' and resid 103 through 112 removed outlier: 3.571A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AF1, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.074A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AF3, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.011A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.645A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 957 through 961 removed outlier: 6.625A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1025 through 1026 Processing sheet with id=AF7, first strand: chain 'J' and resid 1098 through 1099 Processing sheet with id=AF8, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.528A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AG1, first strand: chain 'J' and resid 1279 through 1281 1322 hydrogen bonds defined for protein. 3675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6209 1.32 - 1.44: 9378 1.44 - 1.57: 20808 1.57 - 1.69: 221 1.69 - 1.81: 249 Bond restraints: 36865 Sorted by residual: bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.26e+01 bond pdb=" C4 ATP A2000 " pdb=" N9 ATP A2000 " ideal model delta sigma weight residual 1.374 1.317 0.057 1.00e-02 1.00e+04 3.19e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.465 -0.056 1.00e-02 1.00e+04 3.18e+01 bond pdb=" CA HIS A 120 " pdb=" C HIS A 120 " ideal model delta sigma weight residual 1.529 1.478 0.052 9.30e-03 1.16e+04 3.07e+01 bond pdb=" C5 ATP A2000 " pdb=" N7 ATP A2000 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.05e+01 ... (remaining 36860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 49969 4.33 - 8.66: 330 8.66 - 12.98: 28 12.98 - 17.31: 2 17.31 - 21.64: 2 Bond angle restraints: 50331 Sorted by residual: angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 118.23 21.64 1.00e+00 1.00e+00 4.68e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 116.04 20.79 1.00e+00 1.00e+00 4.32e+02 angle pdb=" N VAL G 14 " pdb=" CA VAL G 14 " pdb=" C VAL G 14 " ideal model delta sigma weight residual 110.72 124.07 -13.35 1.01e+00 9.80e-01 1.75e+02 angle pdb=" N VAL I1186 " pdb=" CA VAL I1186 " pdb=" C VAL I1186 " ideal model delta sigma weight residual 110.42 120.26 -9.84 9.60e-01 1.09e+00 1.05e+02 angle pdb=" N LEU A 474 " pdb=" CA LEU A 474 " pdb=" C LEU A 474 " ideal model delta sigma weight residual 109.15 95.62 13.53 1.44e+00 4.82e-01 8.83e+01 ... (remaining 50326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 21498 35.25 - 70.50: 794 70.50 - 105.75: 47 105.75 - 141.00: 2 141.00 - 176.24: 1 Dihedral angle restraints: 22342 sinusoidal: 9913 harmonic: 12429 Sorted by residual: dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASN I 235 " pdb=" C ASN I 235 " pdb=" N LYS I 236 " pdb=" CA LYS I 236 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 22339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5057 0.088 - 0.176: 623 0.176 - 0.264: 43 0.264 - 0.352: 9 0.352 - 0.440: 7 Chirality restraints: 5739 Sorted by residual: chirality pdb=" CA LEU A 474 " pdb=" N LEU A 474 " pdb=" C LEU A 474 " pdb=" CB LEU A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ALA A 475 " pdb=" N ALA A 475 " pdb=" C ALA A 475 " pdb=" CB ALA A 475 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASN A 473 " pdb=" N ASN A 473 " pdb=" C ASN A 473 " pdb=" CB ASN A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5736 not shown) Planarity restraints: 6200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 117 " -0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C VAL A 117 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 117 " -0.033 2.00e-02 2.50e+03 pdb=" N CYS A 118 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 119 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C PRO A 119 " -0.085 2.00e-02 2.50e+03 pdb=" O PRO A 119 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS A 120 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 204 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO I 205 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO I 205 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO I 205 " -0.058 5.00e-02 4.00e+02 ... (remaining 6197 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 337 2.55 - 3.14: 28618 3.14 - 3.73: 56230 3.73 - 4.31: 78243 4.31 - 4.90: 129981 Nonbonded interactions: 293409 Sorted by model distance: nonbonded pdb=" O3G ATP A2000 " pdb="MG MG A2001 " model vdw 1.966 2.170 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.967 2.170 nonbonded pdb=" CB GLU J 211 " pdb=" OP2 DG P 3 " model vdw 2.013 3.440 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.028 2.170 nonbonded pdb=" OD1 ASP G 15 " pdb=" N ILE G 16 " model vdw 2.042 3.120 ... (remaining 293404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 39.240 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.010 0.114 36872 Z= 0.457 Angle : 1.025 21.639 50337 Z= 0.584 Chirality : 0.060 0.440 5739 Planarity : 0.006 0.108 6200 Dihedral : 17.096 176.244 14330 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.08 % Favored : 90.68 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.12), residues: 4294 helix: -0.90 (0.13), residues: 1496 sheet: -1.77 (0.20), residues: 605 loop : -2.15 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1007 TYR 0.036 0.003 TYR G 177 PHE 0.033 0.003 PHE J 620 TRP 0.022 0.003 TRP J1193 HIS 0.013 0.002 HIS A 948 Details of bonding type rmsd covalent geometry : bond 0.01031 (36865) covalent geometry : angle 1.02198 (50331) hydrogen bonds : bond 0.14172 ( 1440) hydrogen bonds : angle 6.27185 ( 3915) metal coordination : bond 0.01716 ( 7) metal coordination : angle 6.92963 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 431 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8551 (mp) cc_final: 0.8320 (tt) REVERT: A 731 GLU cc_start: 0.8544 (pp20) cc_final: 0.8157 (pp20) REVERT: A 937 GLU cc_start: 0.7560 (pt0) cc_final: 0.7176 (pp20) REVERT: A 1078 LEU cc_start: 0.8633 (tt) cc_final: 0.8326 (tt) REVERT: A 1121 PHE cc_start: 0.6479 (p90) cc_final: 0.6060 (p90) REVERT: G 127 GLN cc_start: 0.8113 (pm20) cc_final: 0.7912 (pm20) REVERT: I 210 LEU cc_start: 0.8421 (mm) cc_final: 0.8218 (mm) REVERT: I 477 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6792 (mm-30) REVERT: I 741 MET cc_start: 0.8335 (mmt) cc_final: 0.8130 (mmm) REVERT: I 842 ASP cc_start: 0.7263 (t0) cc_final: 0.6801 (p0) REVERT: I 958 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8810 (ttmm) REVERT: J 267 ASP cc_start: 0.8187 (t0) cc_final: 0.7863 (t0) REVERT: J 304 ASP cc_start: 0.8580 (t0) cc_final: 0.8364 (t0) REVERT: J 1174 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7226 (mtm-85) REVERT: K 54 ILE cc_start: 0.8935 (mm) cc_final: 0.8701 (mm) REVERT: K 69 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7333 (ttm-80) outliers start: 6 outliers final: 5 residues processed: 436 average time/residue: 0.2296 time to fit residues: 162.3490 Evaluate side-chains 361 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 356 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 710 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 0.0270 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN A 515 ASN A 539 ASN A 574 GLN A 648 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN G 37 HIS H 227 GLN I 69 GLN I 273 HIS ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102708 restraints weight = 58494.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101518 restraints weight = 53751.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102196 restraints weight = 65451.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102851 restraints weight = 41383.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103162 restraints weight = 35889.326| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36872 Z= 0.154 Angle : 0.644 11.325 50337 Z= 0.337 Chirality : 0.044 0.195 5739 Planarity : 0.005 0.078 6200 Dihedral : 15.713 177.172 6001 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.50 % Favored : 93.36 % Rotamer: Outliers : 0.63 % Allowed : 7.56 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.12), residues: 4294 helix: -0.24 (0.13), residues: 1548 sheet: -1.56 (0.21), residues: 592 loop : -2.03 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1140 TYR 0.018 0.001 TYR G 177 PHE 0.016 0.001 PHE I 514 TRP 0.012 0.001 TRP A 260 HIS 0.013 0.001 HIS A 918 Details of bonding type rmsd covalent geometry : bond 0.00346 (36865) covalent geometry : angle 0.64228 (50331) hydrogen bonds : bond 0.04549 ( 1440) hydrogen bonds : angle 4.92236 ( 3915) metal coordination : bond 0.00799 ( 7) metal coordination : angle 4.65847 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 430 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 513 TYR cc_start: 0.8306 (m-80) cc_final: 0.8100 (m-80) REVERT: A 731 GLU cc_start: 0.8375 (pp20) cc_final: 0.8122 (pp20) REVERT: A 765 MET cc_start: 0.8209 (ttp) cc_final: 0.7922 (ttp) REVERT: A 927 GLN cc_start: 0.7677 (mp10) cc_final: 0.7323 (mp10) REVERT: A 1121 PHE cc_start: 0.6217 (p90) cc_final: 0.5874 (p90) REVERT: G 86 LYS cc_start: 0.8800 (tttm) cc_final: 0.8572 (tttm) REVERT: I 17 LYS cc_start: 0.8679 (mppt) cc_final: 0.8296 (mptt) REVERT: I 434 ASP cc_start: 0.7627 (m-30) cc_final: 0.7223 (m-30) REVERT: I 477 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7293 (mm-30) REVERT: I 1066 MET cc_start: 0.9013 (ptp) cc_final: 0.8803 (ptp) REVERT: I 1206 THR cc_start: 0.9207 (t) cc_final: 0.8992 (m) REVERT: J 267 ASP cc_start: 0.7885 (t0) cc_final: 0.7597 (t0) REVERT: J 478 LEU cc_start: 0.9164 (mt) cc_final: 0.8868 (mt) REVERT: J 922 SER cc_start: 0.9356 (m) cc_final: 0.9145 (m) REVERT: J 1040 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.4725 (ttp) REVERT: J 1174 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7513 (mtm180) REVERT: K 69 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7331 (ttm-80) outliers start: 23 outliers final: 11 residues processed: 440 average time/residue: 0.2235 time to fit residues: 160.4977 Evaluate side-chains 381 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 369 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 1040 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 167 optimal weight: 5.9990 chunk 426 optimal weight: 0.5980 chunk 200 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 337 optimal weight: 3.9990 chunk 419 optimal weight: 3.9990 chunk 46 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 515 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 792 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103825 restraints weight = 58527.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102958 restraints weight = 53981.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103596 restraints weight = 62808.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104270 restraints weight = 41708.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104436 restraints weight = 36018.789| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36872 Z= 0.131 Angle : 0.589 11.517 50337 Z= 0.306 Chirality : 0.042 0.181 5739 Planarity : 0.004 0.067 6200 Dihedral : 15.492 177.815 5993 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.43 % Favored : 93.43 % Rotamer: Outliers : 1.52 % Allowed : 11.11 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 4294 helix: 0.28 (0.13), residues: 1545 sheet: -1.45 (0.21), residues: 601 loop : -1.92 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1034 TYR 0.018 0.001 TYR G 177 PHE 0.015 0.001 PHE I 337 TRP 0.010 0.001 TRP A 260 HIS 0.011 0.001 HIS A 918 Details of bonding type rmsd covalent geometry : bond 0.00299 (36865) covalent geometry : angle 0.58830 (50331) hydrogen bonds : bond 0.03935 ( 1440) hydrogen bonds : angle 4.49736 ( 3915) metal coordination : bond 0.00629 ( 7) metal coordination : angle 3.08340 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 419 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 TYR cc_start: 0.8275 (m-80) cc_final: 0.7864 (m-80) REVERT: A 1067 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6722 (mmm-85) REVERT: A 1121 PHE cc_start: 0.6334 (p90) cc_final: 0.6067 (p90) REVERT: I 434 ASP cc_start: 0.7742 (m-30) cc_final: 0.7495 (m-30) REVERT: I 461 GLU cc_start: 0.7828 (tt0) cc_final: 0.7581 (tt0) REVERT: I 472 GLU cc_start: 0.8167 (pp20) cc_final: 0.7732 (pt0) REVERT: I 711 ASP cc_start: 0.8052 (m-30) cc_final: 0.7740 (m-30) REVERT: I 1066 MET cc_start: 0.8990 (ptp) cc_final: 0.8742 (ptp) REVERT: I 1174 GLU cc_start: 0.8191 (tp30) cc_final: 0.7905 (tp30) REVERT: I 1206 THR cc_start: 0.9199 (t) cc_final: 0.8965 (m) REVERT: J 45 ASN cc_start: 0.8454 (t0) cc_final: 0.8224 (t0) REVERT: J 47 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.7344 (ptp-170) REVERT: J 111 THR cc_start: 0.9451 (m) cc_final: 0.9053 (p) REVERT: J 267 ASP cc_start: 0.7906 (t0) cc_final: 0.7568 (t0) REVERT: J 478 LEU cc_start: 0.9126 (mt) cc_final: 0.8819 (mt) REVERT: J 500 ILE cc_start: 0.9299 (mm) cc_final: 0.8904 (pt) REVERT: J 922 SER cc_start: 0.9357 (m) cc_final: 0.9156 (m) REVERT: J 1174 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7370 (mtm180) REVERT: J 1276 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7187 (mm-30) outliers start: 55 outliers final: 22 residues processed: 448 average time/residue: 0.2076 time to fit residues: 154.3772 Evaluate side-chains 398 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 375 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 400 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 428 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 431 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1068 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102077 restraints weight = 58792.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100118 restraints weight = 76342.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101396 restraints weight = 82463.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101655 restraints weight = 47968.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102708 restraints weight = 42830.695| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 36872 Z= 0.260 Angle : 0.650 9.468 50337 Z= 0.336 Chirality : 0.045 0.184 5739 Planarity : 0.005 0.061 6200 Dihedral : 15.552 176.697 5993 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 2.04 % Allowed : 13.51 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4294 helix: 0.35 (0.13), residues: 1543 sheet: -1.38 (0.21), residues: 596 loop : -1.89 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 801 TYR 0.019 0.002 TYR G 177 PHE 0.036 0.002 PHE I 828 TRP 0.009 0.002 TRP A 260 HIS 0.010 0.001 HIS A 918 Details of bonding type rmsd covalent geometry : bond 0.00609 (36865) covalent geometry : angle 0.64923 (50331) hydrogen bonds : bond 0.04288 ( 1440) hydrogen bonds : angle 4.54019 ( 3915) metal coordination : bond 0.01218 ( 7) metal coordination : angle 3.26422 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 388 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1121 PHE cc_start: 0.6378 (p90) cc_final: 0.6063 (p90) REVERT: G 86 LYS cc_start: 0.8963 (tttp) cc_final: 0.8573 (tttm) REVERT: I 434 ASP cc_start: 0.7625 (m-30) cc_final: 0.7323 (m-30) REVERT: I 472 GLU cc_start: 0.8110 (pp20) cc_final: 0.7689 (pt0) REVERT: I 711 ASP cc_start: 0.8088 (m-30) cc_final: 0.7837 (m-30) REVERT: I 814 ASP cc_start: 0.8321 (m-30) cc_final: 0.8119 (m-30) REVERT: I 859 GLU cc_start: 0.6694 (tp30) cc_final: 0.6294 (tp30) REVERT: I 1174 GLU cc_start: 0.8178 (tp30) cc_final: 0.7894 (tp30) REVERT: I 1243 MET cc_start: 0.8904 (ttp) cc_final: 0.8624 (ttp) REVERT: I 1327 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (mp) REVERT: J 45 ASN cc_start: 0.8451 (t0) cc_final: 0.8179 (t0) REVERT: J 47 ARG cc_start: 0.7604 (ptp-110) cc_final: 0.7244 (ptp-110) REVERT: J 111 THR cc_start: 0.9425 (m) cc_final: 0.9031 (p) REVERT: J 188 LEU cc_start: 0.8922 (tt) cc_final: 0.8641 (tt) REVERT: J 267 ASP cc_start: 0.7935 (t0) cc_final: 0.7599 (t0) REVERT: J 478 LEU cc_start: 0.9190 (mt) cc_final: 0.8888 (mt) REVERT: J 500 ILE cc_start: 0.9341 (mm) cc_final: 0.8924 (pt) REVERT: J 712 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7721 (pp30) REVERT: J 1146 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7708 (mm-30) outliers start: 74 outliers final: 47 residues processed: 434 average time/residue: 0.2101 time to fit residues: 151.4626 Evaluate side-chains 415 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 366 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 413 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 403 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102127 restraints weight = 58474.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101004 restraints weight = 53985.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101749 restraints weight = 63647.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102291 restraints weight = 41370.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102509 restraints weight = 36316.247| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36872 Z= 0.165 Angle : 0.599 10.748 50337 Z= 0.309 Chirality : 0.043 0.216 5739 Planarity : 0.004 0.058 6200 Dihedral : 15.456 177.472 5993 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 2.10 % Allowed : 14.34 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4294 helix: 0.54 (0.13), residues: 1551 sheet: -1.33 (0.21), residues: 605 loop : -1.82 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 170 TYR 0.023 0.001 TYR H 177 PHE 0.023 0.001 PHE I 828 TRP 0.010 0.001 TRP J1193 HIS 0.009 0.001 HIS A 918 Details of bonding type rmsd covalent geometry : bond 0.00382 (36865) covalent geometry : angle 0.59848 (50331) hydrogen bonds : bond 0.03909 ( 1440) hydrogen bonds : angle 4.42967 ( 3915) metal coordination : bond 0.00775 ( 7) metal coordination : angle 3.15469 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 389 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LYS cc_start: 0.8507 (mttp) cc_final: 0.8199 (mtpp) REVERT: A 1121 PHE cc_start: 0.6387 (p90) cc_final: 0.6101 (p90) REVERT: I 434 ASP cc_start: 0.7661 (m-30) cc_final: 0.7446 (m-30) REVERT: I 472 GLU cc_start: 0.8218 (pp20) cc_final: 0.7744 (pt0) REVERT: I 477 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7339 (mm-30) REVERT: I 711 ASP cc_start: 0.8052 (m-30) cc_final: 0.7783 (m-30) REVERT: I 814 ASP cc_start: 0.8287 (m-30) cc_final: 0.8065 (m-30) REVERT: I 859 GLU cc_start: 0.6746 (tp30) cc_final: 0.6314 (tp30) REVERT: I 954 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8776 (mtpp) REVERT: I 1174 GLU cc_start: 0.8221 (tp30) cc_final: 0.7889 (tp30) REVERT: I 1243 MET cc_start: 0.8945 (ttp) cc_final: 0.8655 (ttp) REVERT: I 1327 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8522 (mp) REVERT: J 45 ASN cc_start: 0.8503 (t0) cc_final: 0.8242 (t0) REVERT: J 47 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7427 (ptp-110) REVERT: J 111 THR cc_start: 0.9452 (m) cc_final: 0.9030 (p) REVERT: J 188 LEU cc_start: 0.8859 (tt) cc_final: 0.8565 (tt) REVERT: J 267 ASP cc_start: 0.7958 (t0) cc_final: 0.7591 (t0) REVERT: J 478 LEU cc_start: 0.9116 (mt) cc_final: 0.8795 (mt) REVERT: J 500 ILE cc_start: 0.9295 (mm) cc_final: 0.8890 (pt) REVERT: J 712 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7914 (pp30) REVERT: J 1040 MET cc_start: 0.4841 (ttp) cc_final: 0.4583 (ttm) REVERT: J 1174 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7325 (mtm180) outliers start: 76 outliers final: 49 residues processed: 437 average time/residue: 0.2149 time to fit residues: 156.2937 Evaluate side-chains 419 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 99 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 408 optimal weight: 0.0870 chunk 389 optimal weight: 20.0000 chunk 412 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 664 GLN I 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097452 restraints weight = 58889.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099508 restraints weight = 40042.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099685 restraints weight = 23937.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100018 restraints weight = 20774.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100101 restraints weight = 19572.321| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36872 Z= 0.119 Angle : 0.568 11.318 50337 Z= 0.293 Chirality : 0.042 0.212 5739 Planarity : 0.004 0.057 6200 Dihedral : 15.326 177.693 5993 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 1.93 % Allowed : 15.58 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4294 helix: 0.73 (0.13), residues: 1554 sheet: -1.21 (0.21), residues: 617 loop : -1.75 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 170 TYR 0.022 0.001 TYR H 177 PHE 0.018 0.001 PHE I 828 TRP 0.017 0.001 TRP J1193 HIS 0.010 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00269 (36865) covalent geometry : angle 0.56720 (50331) hydrogen bonds : bond 0.03663 ( 1440) hydrogen bonds : angle 4.27214 ( 3915) metal coordination : bond 0.00460 ( 7) metal coordination : angle 2.61618 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 415 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 CYS cc_start: 0.7224 (p) cc_final: 0.6989 (p) REVERT: A 174 MET cc_start: 0.5490 (tmm) cc_final: 0.5117 (tmm) REVERT: A 959 LEU cc_start: 0.9524 (tp) cc_final: 0.9234 (tp) REVERT: A 1121 PHE cc_start: 0.6526 (p90) cc_final: 0.6246 (p90) REVERT: I 126 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7779 (mm-30) REVERT: I 472 GLU cc_start: 0.8410 (pp20) cc_final: 0.7889 (pt0) REVERT: I 477 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7457 (mm-30) REVERT: I 711 ASP cc_start: 0.8024 (m-30) cc_final: 0.7662 (m-30) REVERT: I 859 GLU cc_start: 0.6961 (tp30) cc_final: 0.6453 (tp30) REVERT: I 1034 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.8052 (mtp85) REVERT: I 1174 GLU cc_start: 0.8244 (tp30) cc_final: 0.7883 (tp30) REVERT: I 1178 LYS cc_start: 0.9247 (mtmt) cc_final: 0.9018 (mtpp) REVERT: I 1243 MET cc_start: 0.9006 (ttp) cc_final: 0.8715 (ttp) REVERT: J 29 MET cc_start: 0.8345 (ttp) cc_final: 0.8105 (ttp) REVERT: J 45 ASN cc_start: 0.8615 (t0) cc_final: 0.8381 (t0) REVERT: J 47 ARG cc_start: 0.7881 (ptp-110) cc_final: 0.7575 (ptp-110) REVERT: J 111 THR cc_start: 0.9501 (m) cc_final: 0.9032 (p) REVERT: J 188 LEU cc_start: 0.8620 (tt) cc_final: 0.8148 (tt) REVERT: J 267 ASP cc_start: 0.8123 (t0) cc_final: 0.7721 (t0) REVERT: J 478 LEU cc_start: 0.8976 (mt) cc_final: 0.8622 (mt) REVERT: J 500 ILE cc_start: 0.9222 (mm) cc_final: 0.8856 (pt) REVERT: J 712 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7935 (pp30) REVERT: J 1146 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7895 (mm-30) REVERT: J 1174 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7272 (mtm180) REVERT: J 1275 LEU cc_start: 0.8618 (tp) cc_final: 0.8307 (tt) REVERT: J 1327 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8146 (mt-10) outliers start: 70 outliers final: 50 residues processed: 455 average time/residue: 0.2023 time to fit residues: 154.3221 Evaluate side-chains 429 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 378 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 288 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 359 optimal weight: 3.9990 chunk 375 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 354 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 515 ASN A 574 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095791 restraints weight = 59753.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097291 restraints weight = 39435.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097626 restraints weight = 25666.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097904 restraints weight = 22510.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098060 restraints weight = 21292.752| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36872 Z= 0.188 Angle : 0.598 10.509 50337 Z= 0.308 Chirality : 0.043 0.243 5739 Planarity : 0.004 0.055 6200 Dihedral : 15.340 176.722 5993 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.82 % Favored : 93.08 % Rotamer: Outliers : 1.99 % Allowed : 16.19 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4294 helix: 0.77 (0.13), residues: 1553 sheet: -1.23 (0.21), residues: 608 loop : -1.72 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 170 TYR 0.022 0.001 TYR H 177 PHE 0.022 0.001 PHE I 828 TRP 0.015 0.001 TRP J1193 HIS 0.011 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00441 (36865) covalent geometry : angle 0.59725 (50331) hydrogen bonds : bond 0.03825 ( 1440) hydrogen bonds : angle 4.30253 ( 3915) metal coordination : bond 0.00883 ( 7) metal coordination : angle 2.93320 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 381 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1121 PHE cc_start: 0.6539 (p90) cc_final: 0.6241 (p90) REVERT: I 126 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7864 (mm-30) REVERT: I 472 GLU cc_start: 0.8436 (pp20) cc_final: 0.7919 (pt0) REVERT: I 477 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7517 (mm-30) REVERT: I 711 ASP cc_start: 0.8040 (m-30) cc_final: 0.7703 (m-30) REVERT: I 859 GLU cc_start: 0.7030 (tp30) cc_final: 0.6512 (tp30) REVERT: I 1174 GLU cc_start: 0.8279 (tp30) cc_final: 0.7911 (tp30) REVERT: I 1243 MET cc_start: 0.9026 (ttp) cc_final: 0.8718 (ttp) REVERT: J 29 MET cc_start: 0.8473 (ttp) cc_final: 0.8247 (ttp) REVERT: J 45 ASN cc_start: 0.8586 (t0) cc_final: 0.8354 (t0) REVERT: J 47 ARG cc_start: 0.7936 (ptp-110) cc_final: 0.7642 (ptp-110) REVERT: J 111 THR cc_start: 0.9485 (m) cc_final: 0.9011 (p) REVERT: J 213 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6906 (tttm) REVERT: J 267 ASP cc_start: 0.8182 (t0) cc_final: 0.7781 (t0) REVERT: J 478 LEU cc_start: 0.9011 (mt) cc_final: 0.8663 (mt) REVERT: J 500 ILE cc_start: 0.9236 (mm) cc_final: 0.8857 (pt) REVERT: J 712 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7884 (pp30) REVERT: J 1040 MET cc_start: 0.5359 (ttp) cc_final: 0.4743 (ttm) REVERT: J 1146 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7897 (mm-30) REVERT: J 1174 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7327 (mtm180) REVERT: J 1275 LEU cc_start: 0.8552 (tp) cc_final: 0.8266 (tt) REVERT: J 1327 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8138 (mt-10) REVERT: K 55 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7342 (mt-10) outliers start: 72 outliers final: 56 residues processed: 423 average time/residue: 0.2077 time to fit residues: 146.8229 Evaluate side-chains 423 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 350 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 245 optimal weight: 0.2980 chunk 431 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 416 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 426 optimal weight: 4.9990 chunk 395 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 515 ASN G 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101855 restraints weight = 58375.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100379 restraints weight = 55322.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101058 restraints weight = 66684.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101671 restraints weight = 40704.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102332 restraints weight = 35041.072| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36872 Z= 0.201 Angle : 0.617 10.362 50337 Z= 0.317 Chirality : 0.044 0.253 5739 Planarity : 0.004 0.060 6200 Dihedral : 15.360 176.103 5993 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 2.15 % Allowed : 16.71 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4294 helix: 0.77 (0.13), residues: 1550 sheet: -1.14 (0.21), residues: 595 loop : -1.74 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1034 TYR 0.027 0.001 TYR H 177 PHE 0.019 0.001 PHE I1270 TRP 0.016 0.001 TRP J1193 HIS 0.010 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00471 (36865) covalent geometry : angle 0.61641 (50331) hydrogen bonds : bond 0.03894 ( 1440) hydrogen bonds : angle 4.35002 ( 3915) metal coordination : bond 0.00947 ( 7) metal coordination : angle 3.32034 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 378 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.2825 (t80) cc_final: 0.2150 (t80) REVERT: A 1121 PHE cc_start: 0.6383 (p90) cc_final: 0.6126 (p90) REVERT: I 126 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7831 (tp30) REVERT: I 472 GLU cc_start: 0.8260 (pp20) cc_final: 0.7789 (pt0) REVERT: I 711 ASP cc_start: 0.7960 (m-30) cc_final: 0.7648 (m-30) REVERT: I 1034 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7933 (mtp85) REVERT: I 1174 GLU cc_start: 0.8165 (tp30) cc_final: 0.7859 (tp30) REVERT: I 1243 MET cc_start: 0.8970 (ttp) cc_final: 0.8663 (ttp) REVERT: J 29 MET cc_start: 0.8342 (ttp) cc_final: 0.8141 (ttp) REVERT: J 45 ASN cc_start: 0.8527 (t0) cc_final: 0.8264 (t0) REVERT: J 47 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7504 (ptp-110) REVERT: J 111 THR cc_start: 0.9438 (m) cc_final: 0.9014 (p) REVERT: J 213 LYS cc_start: 0.7334 (mtpt) cc_final: 0.7021 (tttm) REVERT: J 267 ASP cc_start: 0.7979 (t0) cc_final: 0.7603 (t0) REVERT: J 478 LEU cc_start: 0.9117 (mt) cc_final: 0.8773 (mt) REVERT: J 500 ILE cc_start: 0.9264 (mm) cc_final: 0.8920 (pt) REVERT: J 712 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7873 (pp30) REVERT: J 1040 MET cc_start: 0.5378 (ttp) cc_final: 0.5176 (ttp) REVERT: J 1146 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7828 (mm-30) REVERT: J 1174 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7346 (mtm180) REVERT: J 1275 LEU cc_start: 0.8513 (tp) cc_final: 0.8288 (tt) REVERT: J 1327 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8104 (mt-10) outliers start: 78 outliers final: 66 residues processed: 425 average time/residue: 0.2171 time to fit residues: 151.9490 Evaluate side-chains 435 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 368 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 4.9990 chunk 114 optimal weight: 0.0070 chunk 332 optimal weight: 0.8980 chunk 410 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 347 optimal weight: 2.9990 chunk 418 optimal weight: 10.0000 chunk 378 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 420 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 515 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102237 restraints weight = 58627.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100731 restraints weight = 55607.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101635 restraints weight = 64104.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102037 restraints weight = 39228.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102829 restraints weight = 34845.197| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36872 Z= 0.186 Angle : 0.618 10.636 50337 Z= 0.316 Chirality : 0.043 0.212 5739 Planarity : 0.004 0.061 6200 Dihedral : 15.335 175.639 5993 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 2.23 % Allowed : 17.32 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.13), residues: 4294 helix: 0.81 (0.13), residues: 1548 sheet: -1.13 (0.21), residues: 590 loop : -1.71 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 170 TYR 0.027 0.001 TYR H 177 PHE 0.023 0.001 PHE I1270 TRP 0.033 0.002 TRP A1134 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00435 (36865) covalent geometry : angle 0.61651 (50331) hydrogen bonds : bond 0.03851 ( 1440) hydrogen bonds : angle 4.33225 ( 3915) metal coordination : bond 0.00874 ( 7) metal coordination : angle 3.27962 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 379 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.2725 (t80) cc_final: 0.2404 (t80) REVERT: A 1121 PHE cc_start: 0.6502 (p90) cc_final: 0.6212 (p90) REVERT: I 126 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7791 (tp30) REVERT: I 472 GLU cc_start: 0.8239 (pp20) cc_final: 0.7775 (pt0) REVERT: I 477 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7419 (mm-30) REVERT: I 711 ASP cc_start: 0.7941 (m-30) cc_final: 0.7634 (m-30) REVERT: I 1034 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7932 (mtp85) REVERT: I 1174 GLU cc_start: 0.8148 (tp30) cc_final: 0.7847 (tp30) REVERT: I 1243 MET cc_start: 0.8960 (ttp) cc_final: 0.8655 (ttp) REVERT: J 29 MET cc_start: 0.8309 (ttp) cc_final: 0.7954 (ttp) REVERT: J 45 ASN cc_start: 0.8529 (t0) cc_final: 0.8265 (t0) REVERT: J 111 THR cc_start: 0.9429 (m) cc_final: 0.9015 (p) REVERT: J 188 LEU cc_start: 0.8850 (tt) cc_final: 0.8634 (tt) REVERT: J 213 LYS cc_start: 0.7346 (mtpt) cc_final: 0.7055 (tttm) REVERT: J 267 ASP cc_start: 0.7952 (t0) cc_final: 0.7589 (t0) REVERT: J 478 LEU cc_start: 0.9102 (mt) cc_final: 0.8764 (mt) REVERT: J 500 ILE cc_start: 0.9242 (mm) cc_final: 0.8890 (pt) REVERT: J 712 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7848 (pp30) REVERT: J 1146 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7775 (mm-30) REVERT: J 1174 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7328 (mtm180) REVERT: J 1275 LEU cc_start: 0.8438 (tp) cc_final: 0.8008 (tt) REVERT: J 1327 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8105 (mt-10) outliers start: 81 outliers final: 70 residues processed: 428 average time/residue: 0.2103 time to fit residues: 150.1812 Evaluate side-chains 438 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 367 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 225 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 391 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 515 ASN A1137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101154 restraints weight = 58617.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099661 restraints weight = 56800.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100417 restraints weight = 65858.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100992 restraints weight = 40548.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101590 restraints weight = 35275.058| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36872 Z= 0.229 Angle : 0.652 12.842 50337 Z= 0.332 Chirality : 0.044 0.223 5739 Planarity : 0.004 0.061 6200 Dihedral : 15.380 174.655 5993 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 2.18 % Allowed : 17.37 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4294 helix: 0.75 (0.13), residues: 1551 sheet: -1.19 (0.21), residues: 595 loop : -1.71 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 170 TYR 0.018 0.002 TYR H 177 PHE 0.027 0.002 PHE I1270 TRP 0.027 0.002 TRP A1134 HIS 0.010 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00536 (36865) covalent geometry : angle 0.65102 (50331) hydrogen bonds : bond 0.04026 ( 1440) hydrogen bonds : angle 4.39571 ( 3915) metal coordination : bond 0.01096 ( 7) metal coordination : angle 3.64171 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 368 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1121 PHE cc_start: 0.6486 (p90) cc_final: 0.6236 (p90) REVERT: H 182 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.7973 (ttt-90) REVERT: I 126 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7780 (tp30) REVERT: I 472 GLU cc_start: 0.8246 (pp20) cc_final: 0.7784 (pt0) REVERT: I 711 ASP cc_start: 0.7974 (m-30) cc_final: 0.7677 (m-30) REVERT: I 1034 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7935 (mtp85) REVERT: I 1174 GLU cc_start: 0.8164 (tp30) cc_final: 0.7864 (tp30) REVERT: I 1243 MET cc_start: 0.8959 (ttp) cc_final: 0.8662 (ttp) REVERT: J 29 MET cc_start: 0.8349 (ttp) cc_final: 0.8141 (ttp) REVERT: J 45 ASN cc_start: 0.8571 (t0) cc_final: 0.8333 (t0) REVERT: J 188 LEU cc_start: 0.8864 (tt) cc_final: 0.8647 (tt) REVERT: J 267 ASP cc_start: 0.7970 (t0) cc_final: 0.7617 (t0) REVERT: J 478 LEU cc_start: 0.9127 (mt) cc_final: 0.8798 (mt) REVERT: J 500 ILE cc_start: 0.9243 (mm) cc_final: 0.8847 (pt) REVERT: J 712 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7829 (pp30) REVERT: J 1146 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7740 (mm-30) REVERT: J 1174 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7374 (mtm-85) REVERT: J 1275 LEU cc_start: 0.8354 (tp) cc_final: 0.7901 (tt) outliers start: 79 outliers final: 71 residues processed: 416 average time/residue: 0.2044 time to fit residues: 142.9734 Evaluate side-chains 438 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 366 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 413 optimal weight: 3.9990 chunk 403 optimal weight: 0.9990 chunk 320 optimal weight: 2.9990 chunk 418 optimal weight: 0.0170 chunk 183 optimal weight: 2.9990 chunk 334 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 515 ASN A 539 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099005 restraints weight = 58847.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100565 restraints weight = 47161.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100580 restraints weight = 32939.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100836 restraints weight = 28838.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101000 restraints weight = 25466.539| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36872 Z= 0.121 Angle : 0.603 11.852 50337 Z= 0.306 Chirality : 0.042 0.228 5739 Planarity : 0.004 0.059 6200 Dihedral : 15.249 175.270 5993 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 2.07 % Allowed : 17.62 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4294 helix: 0.93 (0.14), residues: 1554 sheet: -1.14 (0.21), residues: 599 loop : -1.61 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 170 TYR 0.040 0.001 TYR J 144 PHE 0.013 0.001 PHE J 141 TRP 0.024 0.001 TRP A1134 HIS 0.008 0.001 HIS A 918 Details of bonding type rmsd covalent geometry : bond 0.00273 (36865) covalent geometry : angle 0.60233 (50331) hydrogen bonds : bond 0.03659 ( 1440) hydrogen bonds : angle 4.23981 ( 3915) metal coordination : bond 0.00444 ( 7) metal coordination : angle 2.86919 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.33 seconds wall clock time: 88 minutes 37.95 seconds (5317.95 seconds total)