Starting phenix.real_space_refine on Sat Mar 7 01:33:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x50_22045/03_2026/6x50_22045.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x50_22045/03_2026/6x50_22045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x50_22045/03_2026/6x50_22045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x50_22045/03_2026/6x50_22045.map" model { file = "/net/cci-nas-00/data/ceres_data/6x50_22045/03_2026/6x50_22045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x50_22045/03_2026/6x50_22045.cif" } resolution = 3.3 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= 0.004 sd= 1.079 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 115 5.49 5 Mg 2 5.21 5 S 142 5.16 5 C 22305 2.51 5 N 6408 2.21 5 O 7103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 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: 36077 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1143, 8946 Classifications: {'peptide': 1143} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 55, 'TRANS': 1087} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 9, 'GLU:plan': 10, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 131 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: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10368 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 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: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 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 23155 SG CYS J 70 25.156 95.249 98.546 1.00 77.00 S ATOM 23169 SG CYS J 72 24.857 98.898 97.662 1.00 82.84 S ATOM 23277 SG CYS J 85 22.759 96.182 95.875 1.00 81.53 S ATOM 23301 SG CYS J 88 26.460 96.310 95.208 1.00 82.01 S ATOM 28977 SG CYS J 814 52.283 34.270 101.823 1.00 62.67 S ATOM 29542 SG CYS J 888 53.584 37.655 101.640 1.00 54.70 S ATOM 29593 SG CYS J 895 52.232 35.964 105.185 1.00 51.27 S ATOM 29614 SG CYS J 898 55.563 35.193 103.372 1.00 46.47 S Time building chain proxies: 7.87, per 1000 atoms: 0.22 Number of scatterers: 36077 At special positions: 0 Unit cell: (139.1, 193.7, 192.4, 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 115 15.00 Mg 2 11.99 O 7103 8.00 N 6408 7.00 C 22305 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 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 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8010 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 55 sheets defined 37.0% alpha, 14.5% beta 54 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 48 through 63 removed outlier: 4.006A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.557A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 220 through 235 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.593A pdb=" N GLN A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 307 Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.813A 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 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.598A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.601A pdb=" N ALA A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.617A pdb=" N LEU A 474 " --> pdb=" O ILE A 471 " (cutoff:3.500A) 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 549 through 553 removed outlier: 3.656A pdb=" N ARG A 552 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 553 " --> pdb=" O TRP A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 563 through 576 removed outlier: 4.168A pdb=" N GLU A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.557A pdb=" N TYR A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 4.115A pdb=" N ASN A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 648 removed outlier: 3.961A pdb=" N VAL A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.701A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 731 through 734 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 760 through 768 removed outlier: 3.735A pdb=" N ALA A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.507A pdb=" N GLU A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 removed outlier: 4.183A pdb=" N ARG A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 858 " --> pdb=" O MET A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 4.180A pdb=" N THR A 873 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 923 through 934 Processing helix chain 'A' and resid 943 through 953 removed outlier: 5.359A pdb=" N GLU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 988 removed outlier: 3.745A pdb=" N ALA A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1001 Processing helix chain 'A' and resid 1019 through 1032 removed outlier: 3.684A pdb=" N ARG A1023 " --> pdb=" O ASP A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.672A 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: 3.865A pdb=" N ASN A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.673A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 229 removed outlier: 3.614A pdb=" N ILE G 217 " --> pdb=" O PRO G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 removed outlier: 4.161A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.935A pdb=" N ASN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.577A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 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: 3.749A 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 288 through 292 removed outlier: 3.768A pdb=" N TYR I 291 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 347 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 378 through 390 removed outlier: 3.837A pdb=" N LEU I 384 " --> pdb=" O ALA I 380 " (cutoff:3.500A) removed outlier: 3.708A 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: 4.002A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.826A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.616A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.820A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 613 removed outlier: 3.581A pdb=" N GLY I 612 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 676 through 687 Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.618A pdb=" N VAL I 708 " --> pdb=" O MET I 704 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 978 Processing helix chain 'I' and resid 979 through 981 No H-bonds generated for 'chain 'I' and resid 979 through 981' Processing helix chain 'I' and resid 987 through 991 removed outlier: 3.650A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.597A pdb=" N GLU I1016 " --> pdb=" O GLU I1012 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS I1027 " --> pdb=" O HIS I1023 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I1029 " --> pdb=" O PHE I1025 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.686A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.537A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.658A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.566A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1171 through 1176 removed outlier: 3.676A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.656A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1280 removed outlier: 3.506A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1290 Processing helix chain 'I' and resid 1297 through 1309 removed outlier: 3.923A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.801A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.661A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.520A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (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 206 Processing helix chain 'J' and resid 211 through 230 removed outlier: 4.174A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.645A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.506A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (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 388 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.892A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.679A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (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 581 removed outlier: 3.838A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.556A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 634 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.543A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.939A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.566A pdb=" N GLY J1071 " --> pdb=" O THR J1068 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1068 through 1072' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.576A pdb=" N LEU J1221 " --> pdb=" O PRO J1217 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1237 removed outlier: 3.838A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1237 through 1242 Processing helix chain 'J' and resid 1243 through 1245 No H-bonds generated for 'chain 'J' and resid 1243 through 1245' Processing helix chain 'J' and resid 1249 through 1259 removed outlier: 4.030A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1289 removed outlier: 3.745A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) Processing helix chain 'J' and resid 1289 through 1294 Processing helix chain 'J' and resid 1310 through 1315 removed outlier: 3.807A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1337 removed outlier: 3.606A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 removed outlier: 3.665A pdb=" N VAL J1353 " --> pdb=" O GLU J1349 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.941A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.501A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.383A pdb=" N VAL A 42 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 108 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 44 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 339 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.263A 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: 6.001A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.961A 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 355 through 356 removed outlier: 6.359A pdb=" N VAL A 386 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN A 410 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE A 427 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.860A pdb=" N TYR A 493 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR A 512 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 495 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE I 117 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LYS I 115 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 680 through 683 removed outlier: 7.320A pdb=" N VAL A 652 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY A 709 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 654 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 726 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU A 754 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 728 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 623 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.162A pdb=" N LYS A 787 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU A 914 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 789 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 883 " --> pdb=" O TYR A 911 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN A 811 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 882 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 839 " --> pdb=" O VAL A 866 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1075 through 1078 Processing sheet with id=AB1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.170A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.587A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.698A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.203A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.640A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.645A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.665A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA H 175 " --> pdb=" O VAL H 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.279A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.516A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.566A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.566A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.106A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.531A pdb=" N TYR I 301 " --> pdb=" O CYS I 311 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.235A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AD3, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AD4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.405A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.258A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD7, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 7.392A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 830 through 841 removed outlier: 4.038A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.617A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.639A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.633A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE5, first strand: chain 'J' and resid 103 through 112 removed outlier: 3.659A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 244 " --> pdb=" O GLY J 103 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE7, first strand: chain 'J' and resid 317 through 319 removed outlier: 6.597A pdb=" N ARG J 322 " --> pdb=" O GLY J 318 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AE9, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AF1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AF2, first strand: chain 'J' and resid 949 through 951 removed outlier: 7.079A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 991 through 996 Processing sheet with id=AF4, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF5, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AF6, first strand: chain 'J' and resid 1098 through 1099 Processing sheet with id=AF7, first strand: chain 'J' and resid 1046 through 1047 removed outlier: 4.054A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 1089 through 1090 removed outlier: 5.919A pdb=" N MET J1095 " --> pdb=" O ILE J1090 " (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 removed outlier: 6.559A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1305 hydrogen bonds defined for protein. 3642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 10.22 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5986 1.28 - 1.41: 8734 1.41 - 1.54: 21603 1.54 - 1.68: 324 1.68 - 1.81: 249 Bond restraints: 36896 Sorted by residual: bond pdb=" C ARG A 782 " pdb=" O ARG A 782 " ideal model delta sigma weight residual 1.236 1.144 0.092 9.80e-03 1.04e+04 8.87e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.92e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.47e+01 bond pdb=" C ALA A 785 " pdb=" O ALA A 785 " ideal model delta sigma weight residual 1.234 1.166 0.068 1.20e-02 6.94e+03 3.23e+01 bond pdb=" CA ALA A 785 " pdb=" C ALA A 785 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.32e-02 5.74e+03 3.06e+01 ... (remaining 36891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 50067 3.79 - 7.57: 297 7.57 - 11.36: 15 11.36 - 15.15: 3 15.15 - 18.94: 3 Bond angle restraints: 50385 Sorted by residual: angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" N ILE A 952 " pdb=" CA ILE A 952 " pdb=" C ILE A 952 " ideal model delta sigma weight residual 110.62 98.42 12.20 1.02e+00 9.61e-01 1.43e+02 angle pdb=" C5 ATP A2000 " pdb=" C4 ATP A2000 " pdb=" N3 ATP A2000 " ideal model delta sigma weight residual 126.80 118.65 8.15 1.00e+00 1.00e+00 6.64e+01 angle pdb=" N3 ATP A2000 " pdb=" C4 ATP A2000 " pdb=" N9 ATP A2000 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 ... (remaining 50380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 21497 35.40 - 70.80: 792 70.80 - 106.20: 55 106.20 - 141.60: 1 141.60 - 176.99: 2 Dihedral angle restraints: 22347 sinusoidal: 9922 harmonic: 12425 Sorted by residual: dihedral pdb=" CA THR J1169 " pdb=" C THR J1169 " pdb=" N LYS J1170 " pdb=" CA LYS J1170 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+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 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+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 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 22344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5600 0.120 - 0.241: 134 0.241 - 0.361: 5 0.361 - 0.482: 4 0.482 - 0.602: 1 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CB ILE I 117 " pdb=" CA ILE I 117 " pdb=" CG1 ILE I 117 " pdb=" CG2 ILE I 117 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" CA ALA A 781 " pdb=" N ALA A 781 " pdb=" C ALA A 781 " pdb=" CB ALA A 781 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA GLU A 951 " pdb=" N GLU A 951 " pdb=" C GLU A 951 " pdb=" CB GLU A 951 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 5741 not shown) Planarity restraints: 6196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 208 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C THR J 208 " 0.064 2.00e-02 2.50e+03 pdb=" O THR J 208 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN J 209 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 759 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A 760 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 783 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ARG A 783 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG A 783 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 784 " -0.017 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 302 2.57 - 3.15: 27642 3.15 - 3.73: 55791 3.73 - 4.32: 77957 4.32 - 4.90: 129757 Nonbonded interactions: 291449 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.985 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 1.991 2.170 nonbonded pdb=" O3G ATP A2000 " pdb="MG MG A2001 " model vdw 2.062 2.170 nonbonded pdb=" O VAL A 117 " pdb=" O CYS A 118 " model vdw 2.069 3.040 nonbonded pdb=" CB ASP A 604 " pdb=" CG2 THR A 778 " model vdw 2.070 3.860 ... (remaining 291444 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 42.420 Find NCS groups from input model: 0.380 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.005 0.092 36904 Z= 0.264 Angle : 0.839 18.935 50397 Z= 0.490 Chirality : 0.052 0.602 5744 Planarity : 0.006 0.075 6196 Dihedral : 17.106 176.994 14337 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.78 % Favored : 91.94 % Rotamer: Outliers : 0.19 % Allowed : 0.28 % Favored : 99.53 % Cbeta Deviations : 0.02 % 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: -2.60 (0.12), residues: 4293 helix: -1.11 (0.13), residues: 1472 sheet: -1.75 (0.20), residues: 627 loop : -2.14 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I1211 TYR 0.034 0.002 TYR H 177 PHE 0.028 0.002 PHE A 172 TRP 0.028 0.002 TRP I 183 HIS 0.017 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00529 (36896) covalent geometry : angle 0.83426 (50385) hydrogen bonds : bond 0.17946 ( 1437) hydrogen bonds : angle 7.14322 ( 3914) metal coordination : bond 0.01060 ( 8) metal coordination : angle 5.88337 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 483 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7787 (pm20) cc_final: 0.7575 (pm20) REVERT: A 298 ASP cc_start: 0.7653 (t70) cc_final: 0.7381 (t0) REVERT: A 311 MET cc_start: 0.7524 (mtm) cc_final: 0.7213 (mtp) REVERT: A 1067 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8050 (tmm-80) REVERT: I 39 ILE cc_start: 0.8869 (pt) cc_final: 0.8636 (pt) REVERT: I 210 LEU cc_start: 0.7599 (mt) cc_final: 0.7396 (mt) REVERT: I 337 PHE cc_start: 0.8457 (t80) cc_final: 0.8099 (t80) REVERT: I 550 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8606 (p) REVERT: I 1080 ASN cc_start: 0.8062 (t0) cc_final: 0.7854 (t0) REVERT: J 129 ASP cc_start: 0.7874 (t0) cc_final: 0.7538 (t0) REVERT: J 295 GLU cc_start: 0.7640 (tp30) cc_final: 0.7152 (tp30) REVERT: J 634 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7526 (ttm-80) REVERT: J 709 ARG cc_start: 0.6807 (ppt170) cc_final: 0.6467 (ppt170) REVERT: J 725 MET cc_start: 0.8290 (mtp) cc_final: 0.7906 (mtp) REVERT: J 892 PHE cc_start: 0.8414 (m-10) cc_final: 0.8014 (m-10) REVERT: J 1019 ASN cc_start: 0.6190 (m-40) cc_final: 0.5803 (m-40) REVERT: J 1174 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.6956 (ttp80) REVERT: J 1189 MET cc_start: 0.7358 (mmm) cc_final: 0.6830 (mmm) REVERT: J 1334 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 7 outliers final: 4 residues processed: 490 average time/residue: 0.2374 time to fit residues: 187.0255 Evaluate side-chains 387 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 382 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 207 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN I 834 GLN J 294 ASN J 320 ASN J 424 ASN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104998 restraints weight = 49205.796| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.28 r_work: 0.3081 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 36904 Z= 0.254 Angle : 0.671 15.413 50397 Z= 0.350 Chirality : 0.046 0.214 5744 Planarity : 0.005 0.061 6196 Dihedral : 15.594 175.659 6018 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 1.24 % Allowed : 8.04 % Favored : 90.72 % 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: -2.12 (0.12), residues: 4293 helix: -0.53 (0.13), residues: 1516 sheet: -1.62 (0.20), residues: 594 loop : -1.98 (0.12), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 779 TYR 0.016 0.002 TYR A 259 PHE 0.016 0.002 PHE I 514 TRP 0.023 0.002 TRP A1099 HIS 0.013 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00600 (36896) covalent geometry : angle 0.66374 (50385) hydrogen bonds : bond 0.04789 ( 1437) hydrogen bonds : angle 5.09113 ( 3914) metal coordination : bond 0.01305 ( 8) metal coordination : angle 6.47888 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 405 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ASP cc_start: 0.8864 (t70) cc_final: 0.8569 (t0) REVERT: A 931 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: A 1067 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7812 (tmm-80) REVERT: G 62 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: G 75 GLN cc_start: 0.8857 (pt0) cc_final: 0.8587 (tt0) REVERT: H 127 GLN cc_start: 0.9247 (pm20) cc_final: 0.9029 (mp10) REVERT: H 177 TYR cc_start: 0.9185 (m-10) cc_final: 0.8839 (m-10) REVERT: I 210 LEU cc_start: 0.7987 (mt) cc_final: 0.7518 (mt) REVERT: I 337 PHE cc_start: 0.8667 (t80) cc_final: 0.8162 (t80) REVERT: I 339 ASN cc_start: 0.7735 (t0) cc_final: 0.7347 (t0) REVERT: I 618 GLN cc_start: 0.7622 (tt0) cc_final: 0.7377 (tt0) REVERT: I 1197 GLU cc_start: 0.8432 (tt0) cc_final: 0.8112 (tm-30) REVERT: J 129 ASP cc_start: 0.8239 (t0) cc_final: 0.7761 (t0) REVERT: J 245 LEU cc_start: 0.9169 (tp) cc_final: 0.8963 (tp) REVERT: J 295 GLU cc_start: 0.8444 (tp30) cc_final: 0.7806 (tp30) REVERT: J 725 MET cc_start: 0.8790 (mtp) cc_final: 0.8463 (mtp) REVERT: J 822 MET cc_start: 0.7546 (mtm) cc_final: 0.7294 (mtp) REVERT: J 1019 ASN cc_start: 0.7032 (m-40) cc_final: 0.6548 (m-40) REVERT: J 1174 ARG cc_start: 0.6232 (ttp-170) cc_final: 0.5949 (ttp80) REVERT: J 1189 MET cc_start: 0.7354 (mmm) cc_final: 0.6905 (mmm) REVERT: J 1235 ASN cc_start: 0.8356 (m-40) cc_final: 0.7835 (m-40) outliers start: 45 outliers final: 28 residues processed: 439 average time/residue: 0.2465 time to fit residues: 172.2783 Evaluate side-chains 399 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 369 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 1283 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 189 optimal weight: 20.0000 chunk 268 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 349 optimal weight: 0.8980 chunk 311 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 338 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN I 69 GLN J 320 ASN J 365 GLN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1084 GLN J1289 ASN J1367 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109017 restraints weight = 48887.542| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.33 r_work: 0.3126 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36904 Z= 0.132 Angle : 0.565 13.424 50397 Z= 0.295 Chirality : 0.042 0.160 5744 Planarity : 0.004 0.058 6196 Dihedral : 15.413 174.705 6016 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 1.52 % Allowed : 10.86 % Favored : 87.62 % 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: -1.66 (0.12), residues: 4293 helix: -0.04 (0.13), residues: 1529 sheet: -1.41 (0.21), residues: 591 loop : -1.80 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 779 TYR 0.014 0.001 TYR G 177 PHE 0.013 0.001 PHE A 972 TRP 0.013 0.001 TRP J 33 HIS 0.010 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00301 (36896) covalent geometry : angle 0.55941 (50385) hydrogen bonds : bond 0.03979 ( 1437) hydrogen bonds : angle 4.60837 ( 3914) metal coordination : bond 0.00965 ( 8) metal coordination : angle 5.33546 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ASP cc_start: 0.8853 (t70) cc_final: 0.8550 (t0) REVERT: A 426 MET cc_start: 0.9005 (ptm) cc_final: 0.8680 (ptp) REVERT: A 740 GLU cc_start: 0.8402 (mp0) cc_final: 0.7971 (mp0) REVERT: A 770 MET cc_start: 0.8684 (mtt) cc_final: 0.8403 (mpp) REVERT: A 972 PHE cc_start: 0.7906 (t80) cc_final: 0.7112 (t80) REVERT: A 1067 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7847 (tmm-80) REVERT: G 62 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: G 141 SER cc_start: 0.8804 (p) cc_final: 0.8222 (p) REVERT: H 127 GLN cc_start: 0.9210 (pm20) cc_final: 0.9003 (mp10) REVERT: H 177 TYR cc_start: 0.9112 (m-10) cc_final: 0.8860 (m-10) REVERT: I 18 ARG cc_start: 0.8780 (mmt-90) cc_final: 0.8302 (mmt90) REVERT: I 210 LEU cc_start: 0.7774 (mt) cc_final: 0.7138 (mt) REVERT: I 239 MET cc_start: 0.4695 (tmm) cc_final: 0.4358 (tmm) REVERT: I 337 PHE cc_start: 0.8617 (t80) cc_final: 0.8080 (t80) REVERT: I 339 ASN cc_start: 0.7810 (t0) cc_final: 0.7505 (t0) REVERT: I 429 MET cc_start: 0.8472 (mtm) cc_final: 0.8268 (mtt) REVERT: I 446 ASP cc_start: 0.8730 (m-30) cc_final: 0.8328 (t0) REVERT: I 618 GLN cc_start: 0.7605 (tt0) cc_final: 0.7335 (tt0) REVERT: I 1197 GLU cc_start: 0.8332 (tt0) cc_final: 0.8042 (tm-30) REVERT: I 1297 ASP cc_start: 0.8714 (t70) cc_final: 0.8403 (t0) REVERT: J 129 ASP cc_start: 0.8250 (t0) cc_final: 0.7696 (t0) REVERT: J 289 ASP cc_start: 0.8396 (m-30) cc_final: 0.7821 (t0) REVERT: J 294 ASN cc_start: 0.8017 (m-40) cc_final: 0.7472 (m110) REVERT: J 295 GLU cc_start: 0.8279 (tp30) cc_final: 0.7559 (tp30) REVERT: J 548 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (t) REVERT: J 1019 ASN cc_start: 0.6868 (m-40) cc_final: 0.6387 (m-40) REVERT: J 1189 MET cc_start: 0.7367 (mmm) cc_final: 0.6970 (mmm) outliers start: 55 outliers final: 32 residues processed: 458 average time/residue: 0.2376 time to fit residues: 173.3673 Evaluate side-chains 411 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 377 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 435 optimal weight: 2.9990 chunk 436 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 411 optimal weight: 9.9990 chunk 316 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 343 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN A 543 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105632 restraints weight = 48911.356| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.31 r_work: 0.3080 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36904 Z= 0.224 Angle : 0.610 13.308 50397 Z= 0.316 Chirality : 0.044 0.174 5744 Planarity : 0.005 0.053 6196 Dihedral : 15.485 175.572 6016 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 2.02 % Allowed : 12.60 % Favored : 85.39 % 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: -1.56 (0.12), residues: 4293 helix: 0.10 (0.13), residues: 1524 sheet: -1.40 (0.21), residues: 592 loop : -1.76 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 779 TYR 0.015 0.001 TYR A 259 PHE 0.017 0.001 PHE I 545 TRP 0.015 0.001 TRP I 183 HIS 0.013 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00531 (36896) covalent geometry : angle 0.60333 (50385) hydrogen bonds : bond 0.04190 ( 1437) hydrogen bonds : angle 4.55246 ( 3914) metal coordination : bond 0.01212 ( 8) metal coordination : angle 5.77157 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 374 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: A 298 ASP cc_start: 0.8894 (t70) cc_final: 0.8569 (t0) REVERT: A 437 THR cc_start: 0.8608 (p) cc_final: 0.8398 (p) REVERT: A 1067 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7940 (tmm-80) REVERT: G 62 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: G 75 GLN cc_start: 0.8783 (pt0) cc_final: 0.8475 (tt0) REVERT: H 127 GLN cc_start: 0.9205 (pm20) cc_final: 0.8995 (mp10) REVERT: H 177 TYR cc_start: 0.9154 (m-10) cc_final: 0.8873 (m-10) REVERT: H 199 ASP cc_start: 0.8572 (m-30) cc_final: 0.8197 (t0) REVERT: I 210 LEU cc_start: 0.7878 (mt) cc_final: 0.7114 (mt) REVERT: I 239 MET cc_start: 0.4879 (tmm) cc_final: 0.4516 (tmm) REVERT: I 337 PHE cc_start: 0.8639 (t80) cc_final: 0.8113 (t80) REVERT: I 339 ASN cc_start: 0.7749 (t0) cc_final: 0.7464 (t0) REVERT: I 429 MET cc_start: 0.8604 (mtm) cc_final: 0.8336 (mtt) REVERT: I 618 GLN cc_start: 0.7536 (tt0) cc_final: 0.7264 (tt0) REVERT: I 1197 GLU cc_start: 0.8365 (tt0) cc_final: 0.8073 (tm-30) REVERT: I 1297 ASP cc_start: 0.8738 (t70) cc_final: 0.8427 (t0) REVERT: J 129 ASP cc_start: 0.8315 (t0) cc_final: 0.7767 (t0) REVERT: J 159 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (mp) REVERT: J 289 ASP cc_start: 0.8407 (m-30) cc_final: 0.7863 (t0) REVERT: J 295 GLU cc_start: 0.8583 (tp30) cc_final: 0.8154 (tp30) REVERT: J 997 VAL cc_start: 0.7564 (OUTLIER) cc_final: 0.7300 (m) REVERT: J 1188 GLU cc_start: 0.7056 (tt0) cc_final: 0.6848 (tt0) REVERT: J 1189 MET cc_start: 0.7376 (mmm) cc_final: 0.7007 (mmm) REVERT: J 1261 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8486 (pp) outliers start: 73 outliers final: 46 residues processed: 427 average time/residue: 0.2474 time to fit residues: 171.2715 Evaluate side-chains 414 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 150 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 256 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 376 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 356 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106908 restraints weight = 48829.361| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.10 r_work: 0.3107 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36904 Z= 0.185 Angle : 0.580 13.290 50397 Z= 0.301 Chirality : 0.043 0.169 5744 Planarity : 0.004 0.054 6196 Dihedral : 15.421 175.207 6013 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.20 % Rotamer: Outliers : 2.10 % Allowed : 13.67 % Favored : 84.23 % 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: -1.44 (0.13), residues: 4293 helix: 0.21 (0.13), residues: 1533 sheet: -1.35 (0.21), residues: 590 loop : -1.71 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 779 TYR 0.014 0.001 TYR A 259 PHE 0.021 0.001 PHE A 355 TRP 0.013 0.001 TRP I 183 HIS 0.011 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00436 (36896) covalent geometry : angle 0.57422 (50385) hydrogen bonds : bond 0.03981 ( 1437) hydrogen bonds : angle 4.45642 ( 3914) metal coordination : bond 0.01088 ( 8) metal coordination : angle 5.34389 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 388 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: A 298 ASP cc_start: 0.8876 (t70) cc_final: 0.8546 (t0) REVERT: A 1067 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7861 (tmm-80) REVERT: G 62 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: G 75 GLN cc_start: 0.8723 (pt0) cc_final: 0.8419 (tt0) REVERT: G 141 SER cc_start: 0.8761 (p) cc_final: 0.8268 (p) REVERT: H 127 GLN cc_start: 0.9214 (pm20) cc_final: 0.8988 (mp10) REVERT: H 177 TYR cc_start: 0.9101 (m-10) cc_final: 0.8815 (m-10) REVERT: I 18 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8098 (mmt90) REVERT: I 81 ASP cc_start: 0.8385 (p0) cc_final: 0.7828 (p0) REVERT: I 84 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: I 239 MET cc_start: 0.4804 (tmm) cc_final: 0.4441 (tmm) REVERT: I 337 PHE cc_start: 0.8627 (t80) cc_final: 0.8079 (t80) REVERT: I 339 ASN cc_start: 0.7673 (t0) cc_final: 0.7369 (t0) REVERT: I 351 LEU cc_start: 0.8307 (mt) cc_final: 0.8047 (mt) REVERT: I 618 GLN cc_start: 0.7499 (tt0) cc_final: 0.7230 (tt0) REVERT: I 826 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8362 (t0) REVERT: I 1197 GLU cc_start: 0.8304 (tt0) cc_final: 0.7915 (tm-30) REVERT: I 1297 ASP cc_start: 0.8673 (t70) cc_final: 0.8352 (t0) REVERT: J 129 ASP cc_start: 0.8060 (t0) cc_final: 0.7442 (t0) REVERT: J 159 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (mp) REVERT: J 289 ASP cc_start: 0.8320 (m-30) cc_final: 0.7765 (t0) REVERT: J 295 GLU cc_start: 0.8603 (tp30) cc_final: 0.8065 (tp30) REVERT: J 997 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7217 (m) REVERT: J 1189 MET cc_start: 0.7332 (mmm) cc_final: 0.7002 (mmm) REVERT: J 1261 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8368 (pp) outliers start: 76 outliers final: 56 residues processed: 449 average time/residue: 0.2378 time to fit residues: 172.6640 Evaluate side-chains 430 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 367 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 368 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 229 optimal weight: 0.0980 chunk 189 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 413 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 574 GLN G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** 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 = 0.3883 r_free = 0.3883 target = 0.153862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107799 restraints weight = 48709.803| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.29 r_work: 0.3094 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36904 Z= 0.190 Angle : 0.582 13.144 50397 Z= 0.302 Chirality : 0.043 0.167 5744 Planarity : 0.004 0.052 6196 Dihedral : 15.435 175.169 6013 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 2.60 % Allowed : 14.14 % Favored : 83.26 % 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: -1.36 (0.13), residues: 4293 helix: 0.31 (0.14), residues: 1531 sheet: -1.36 (0.21), residues: 596 loop : -1.68 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 779 TYR 0.015 0.001 TYR A 259 PHE 0.018 0.001 PHE J 172 TRP 0.014 0.001 TRP I 183 HIS 0.012 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00449 (36896) covalent geometry : angle 0.57657 (50385) hydrogen bonds : bond 0.03964 ( 1437) hydrogen bonds : angle 4.38938 ( 3914) metal coordination : bond 0.01076 ( 8) metal coordination : angle 5.24038 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 381 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: A 298 ASP cc_start: 0.8905 (t70) cc_final: 0.8572 (t0) REVERT: A 1067 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7853 (tmm-80) REVERT: G 62 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: G 75 GLN cc_start: 0.8736 (pt0) cc_final: 0.8410 (tt0) REVERT: G 141 SER cc_start: 0.8770 (p) cc_final: 0.8288 (p) REVERT: H 127 GLN cc_start: 0.9237 (pm20) cc_final: 0.9005 (mp10) REVERT: H 177 TYR cc_start: 0.9096 (m-10) cc_final: 0.8832 (m-10) REVERT: H 199 ASP cc_start: 0.8509 (m-30) cc_final: 0.7995 (t0) REVERT: I 84 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: I 210 LEU cc_start: 0.7742 (mt) cc_final: 0.6970 (mt) REVERT: I 239 MET cc_start: 0.4813 (tmm) cc_final: 0.4438 (tmm) REVERT: I 337 PHE cc_start: 0.8717 (t80) cc_final: 0.8226 (t80) REVERT: I 339 ASN cc_start: 0.7690 (t0) cc_final: 0.7342 (t0) REVERT: I 351 LEU cc_start: 0.8308 (mt) cc_final: 0.8060 (mt) REVERT: I 410 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8579 (mm) REVERT: I 488 MET cc_start: 0.8951 (mmm) cc_final: 0.8701 (tpt) REVERT: I 618 GLN cc_start: 0.7521 (tt0) cc_final: 0.7248 (tt0) REVERT: I 826 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8307 (t0) REVERT: I 1197 GLU cc_start: 0.8321 (tt0) cc_final: 0.7926 (tm-30) REVERT: I 1297 ASP cc_start: 0.8680 (t70) cc_final: 0.8357 (t0) REVERT: J 129 ASP cc_start: 0.8106 (t0) cc_final: 0.7487 (t0) REVERT: J 159 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8559 (mp) REVERT: J 229 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: J 289 ASP cc_start: 0.8328 (m-30) cc_final: 0.7775 (t0) REVERT: J 294 ASN cc_start: 0.8058 (m-40) cc_final: 0.7471 (m110) REVERT: J 295 GLU cc_start: 0.8637 (tp30) cc_final: 0.8094 (tp30) REVERT: J 837 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8497 (t0) REVERT: J 844 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8039 (p) REVERT: J 997 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7430 (m) REVERT: J 1189 MET cc_start: 0.7334 (mmm) cc_final: 0.6992 (mmm) REVERT: J 1261 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8337 (pp) REVERT: J 1266 ILE cc_start: 0.8193 (mm) cc_final: 0.7973 (mm) outliers start: 94 outliers final: 68 residues processed: 456 average time/residue: 0.2320 time to fit residues: 171.4938 Evaluate side-chains 443 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 364 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 209 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 323 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 363 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 330 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104702 restraints weight = 49013.220| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.40 r_work: 0.3075 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36904 Z= 0.198 Angle : 0.591 13.150 50397 Z= 0.305 Chirality : 0.043 0.173 5744 Planarity : 0.004 0.053 6196 Dihedral : 15.439 175.260 6013 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.15 % Favored : 92.78 % Rotamer: Outliers : 2.79 % Allowed : 14.31 % Favored : 82.90 % 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: 4293 helix: 0.38 (0.14), residues: 1528 sheet: -1.35 (0.21), residues: 596 loop : -1.66 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 779 TYR 0.014 0.001 TYR A 259 PHE 0.017 0.001 PHE I 545 TRP 0.015 0.001 TRP I 183 HIS 0.012 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00467 (36896) covalent geometry : angle 0.58409 (50385) hydrogen bonds : bond 0.03982 ( 1437) hydrogen bonds : angle 4.36670 ( 3914) metal coordination : bond 0.01346 ( 8) metal coordination : angle 5.74615 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 375 time to evaluate : 1.341 Fit side-chains REVERT: A 242 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: A 298 ASP cc_start: 0.8942 (t70) cc_final: 0.8612 (t0) REVERT: A 1067 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7921 (tmm-80) REVERT: G 62 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: G 75 GLN cc_start: 0.8834 (pt0) cc_final: 0.8458 (tt0) REVERT: G 141 SER cc_start: 0.8807 (p) cc_final: 0.8362 (p) REVERT: H 127 GLN cc_start: 0.9250 (pm20) cc_final: 0.9034 (mp10) REVERT: H 177 TYR cc_start: 0.9135 (m-10) cc_final: 0.8926 (m-10) REVERT: H 199 ASP cc_start: 0.8556 (m-30) cc_final: 0.8075 (t0) REVERT: I 18 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8072 (mmt90) REVERT: I 69 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: I 81 ASP cc_start: 0.8562 (p0) cc_final: 0.8059 (p0) REVERT: I 84 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: I 239 MET cc_start: 0.5019 (tmm) cc_final: 0.4791 (tmm) REVERT: I 337 PHE cc_start: 0.8765 (t80) cc_final: 0.8277 (t80) REVERT: I 339 ASN cc_start: 0.7735 (t0) cc_final: 0.7427 (t0) REVERT: I 351 LEU cc_start: 0.8401 (mt) cc_final: 0.8146 (mt) REVERT: I 410 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8616 (mm) REVERT: I 488 MET cc_start: 0.8943 (mmm) cc_final: 0.8710 (tpt) REVERT: I 618 GLN cc_start: 0.7552 (tt0) cc_final: 0.7288 (tt0) REVERT: I 728 ASP cc_start: 0.8346 (t0) cc_final: 0.7992 (t0) REVERT: I 826 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8276 (t0) REVERT: I 1197 GLU cc_start: 0.8370 (tt0) cc_final: 0.8051 (tm-30) REVERT: I 1297 ASP cc_start: 0.8753 (t70) cc_final: 0.8457 (t0) REVERT: J 129 ASP cc_start: 0.8277 (t0) cc_final: 0.7671 (t0) REVERT: J 159 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8675 (mp) REVERT: J 229 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: J 289 ASP cc_start: 0.8421 (m-30) cc_final: 0.7905 (t0) REVERT: J 294 ASN cc_start: 0.8171 (m-40) cc_final: 0.7582 (m110) REVERT: J 295 GLU cc_start: 0.8695 (tp30) cc_final: 0.8179 (tp30) REVERT: J 837 ASP cc_start: 0.9118 (m-30) cc_final: 0.8548 (t0) REVERT: J 844 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8041 (p) REVERT: J 997 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7465 (m) REVERT: J 1189 MET cc_start: 0.7181 (mmm) cc_final: 0.6907 (mmm) REVERT: J 1261 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8433 (pp) REVERT: J 1266 ILE cc_start: 0.8243 (mm) cc_final: 0.8033 (mm) outliers start: 101 outliers final: 73 residues processed: 456 average time/residue: 0.2383 time to fit residues: 176.1467 Evaluate side-chains 450 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 366 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 90 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 411 optimal weight: 0.0030 chunk 317 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 214 optimal weight: 0.5980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107400 restraints weight = 48541.203| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.30 r_work: 0.3095 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36904 Z= 0.129 Angle : 0.554 13.119 50397 Z= 0.287 Chirality : 0.042 0.179 5744 Planarity : 0.004 0.051 6196 Dihedral : 15.334 173.987 6013 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 2.38 % Allowed : 15.11 % Favored : 82.51 % 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: -1.11 (0.13), residues: 4293 helix: 0.57 (0.14), residues: 1530 sheet: -1.22 (0.21), residues: 590 loop : -1.57 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 779 TYR 0.015 0.001 TYR A 590 PHE 0.015 0.001 PHE I 545 TRP 0.012 0.001 TRP I 183 HIS 0.009 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00297 (36896) covalent geometry : angle 0.54795 (50385) hydrogen bonds : bond 0.03612 ( 1437) hydrogen bonds : angle 4.24266 ( 3914) metal coordination : bond 0.01009 ( 8) metal coordination : angle 5.17302 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 396 time to evaluate : 1.318 Fit side-chains REVERT: A 242 GLU cc_start: 0.8601 (pm20) cc_final: 0.8371 (tm-30) REVERT: A 298 ASP cc_start: 0.8941 (t70) cc_final: 0.8617 (t0) REVERT: A 1026 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: A 1067 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7916 (tmm-80) REVERT: G 62 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: G 141 SER cc_start: 0.8913 (p) cc_final: 0.8501 (p) REVERT: H 127 GLN cc_start: 0.9237 (pm20) cc_final: 0.9033 (mp10) REVERT: H 199 ASP cc_start: 0.8413 (m-30) cc_final: 0.7985 (t0) REVERT: I 81 ASP cc_start: 0.8570 (p0) cc_final: 0.7788 (p0) REVERT: I 84 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: I 85 CYS cc_start: 0.9025 (m) cc_final: 0.8593 (m) REVERT: I 239 MET cc_start: 0.5038 (tmm) cc_final: 0.4554 (tmm) REVERT: I 337 PHE cc_start: 0.8690 (t80) cc_final: 0.8201 (t80) REVERT: I 339 ASN cc_start: 0.7714 (t0) cc_final: 0.7490 (t0) REVERT: I 351 LEU cc_start: 0.8283 (mt) cc_final: 0.8017 (mt) REVERT: I 410 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8601 (mm) REVERT: I 618 GLN cc_start: 0.7699 (tt0) cc_final: 0.7405 (tt0) REVERT: I 728 ASP cc_start: 0.8414 (t0) cc_final: 0.8045 (t0) REVERT: I 826 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8317 (t0) REVERT: I 955 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (tp-100) REVERT: I 1096 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8776 (mt) REVERT: J 129 ASP cc_start: 0.8280 (t0) cc_final: 0.7666 (t0) REVERT: J 159 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8644 (mp) REVERT: J 229 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: J 289 ASP cc_start: 0.8350 (m-30) cc_final: 0.7837 (t0) REVERT: J 294 ASN cc_start: 0.8206 (m-40) cc_final: 0.7632 (m110) REVERT: J 295 GLU cc_start: 0.8645 (tp30) cc_final: 0.8073 (tp30) REVERT: J 837 ASP cc_start: 0.9064 (m-30) cc_final: 0.8511 (t0) REVERT: J 844 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7996 (p) REVERT: J 997 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7486 (m) REVERT: J 1165 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: J 1189 MET cc_start: 0.7185 (mmm) cc_final: 0.6938 (mmm) REVERT: J 1261 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8438 (pp) REVERT: J 1266 ILE cc_start: 0.8059 (mm) cc_final: 0.7842 (mm) outliers start: 86 outliers final: 55 residues processed: 465 average time/residue: 0.2365 time to fit residues: 177.8556 Evaluate side-chains 444 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 376 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 129 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 416 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107622 restraints weight = 48710.095| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.31 r_work: 0.3128 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36904 Z= 0.128 Angle : 0.553 13.943 50397 Z= 0.286 Chirality : 0.042 0.185 5744 Planarity : 0.004 0.054 6196 Dihedral : 15.281 173.535 6013 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 2.21 % Allowed : 15.61 % Favored : 82.18 % 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: -0.98 (0.13), residues: 4293 helix: 0.69 (0.14), residues: 1522 sheet: -1.22 (0.21), residues: 595 loop : -1.47 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 779 TYR 0.053 0.001 TYR H 177 PHE 0.011 0.001 PHE J 892 TRP 0.009 0.001 TRP A 260 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00296 (36896) covalent geometry : angle 0.54734 (50385) hydrogen bonds : bond 0.03553 ( 1437) hydrogen bonds : angle 4.17238 ( 3914) metal coordination : bond 0.00981 ( 8) metal coordination : angle 5.28668 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 396 time to evaluate : 1.304 Fit side-chains REVERT: A 298 ASP cc_start: 0.8881 (t70) cc_final: 0.8547 (t0) REVERT: A 740 GLU cc_start: 0.8379 (mp0) cc_final: 0.8000 (mp0) REVERT: A 1026 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: A 1067 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7903 (tmm-80) REVERT: G 10 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8457 (mtmt) REVERT: G 62 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: G 141 SER cc_start: 0.8905 (p) cc_final: 0.8484 (p) REVERT: H 127 GLN cc_start: 0.9231 (pm20) cc_final: 0.9024 (mp10) REVERT: H 199 ASP cc_start: 0.8419 (m-30) cc_final: 0.7986 (t0) REVERT: I 69 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8757 (pt0) REVERT: I 81 ASP cc_start: 0.8546 (p0) cc_final: 0.7730 (p0) REVERT: I 84 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: I 85 CYS cc_start: 0.8996 (m) cc_final: 0.8539 (m) REVERT: I 239 MET cc_start: 0.5050 (tmm) cc_final: 0.4566 (tmm) REVERT: I 337 PHE cc_start: 0.8671 (t80) cc_final: 0.8189 (t80) REVERT: I 351 LEU cc_start: 0.8263 (mt) cc_final: 0.7987 (mt) REVERT: I 410 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8663 (mm) REVERT: I 483 ASP cc_start: 0.8274 (t70) cc_final: 0.7919 (t70) REVERT: I 618 GLN cc_start: 0.7669 (tt0) cc_final: 0.7372 (tt0) REVERT: I 728 ASP cc_start: 0.8349 (t0) cc_final: 0.7998 (t0) REVERT: I 955 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8118 (tp-100) REVERT: I 1096 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8741 (mt) REVERT: J 129 ASP cc_start: 0.8262 (t0) cc_final: 0.7657 (t0) REVERT: J 229 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: J 289 ASP cc_start: 0.8304 (m-30) cc_final: 0.7793 (t0) REVERT: J 294 ASN cc_start: 0.8145 (m-40) cc_final: 0.7560 (m110) REVERT: J 295 GLU cc_start: 0.8628 (tp30) cc_final: 0.8080 (tp30) REVERT: J 837 ASP cc_start: 0.9053 (m-30) cc_final: 0.8503 (t0) REVERT: J 844 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8117 (p) REVERT: J 997 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7473 (m) REVERT: J 1165 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: J 1189 MET cc_start: 0.7175 (mmm) cc_final: 0.6931 (mmm) REVERT: J 1261 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8341 (pp) REVERT: J 1266 ILE cc_start: 0.8028 (mm) cc_final: 0.7820 (mm) outliers start: 80 outliers final: 57 residues processed: 457 average time/residue: 0.2214 time to fit residues: 164.3016 Evaluate side-chains 449 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 380 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 412 optimal weight: 0.0970 chunk 271 optimal weight: 3.9990 chunk 350 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 426 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 308 optimal weight: 0.6980 chunk 429 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107882 restraints weight = 48790.893| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.34 r_work: 0.3125 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36904 Z= 0.133 Angle : 0.557 14.518 50397 Z= 0.287 Chirality : 0.042 0.362 5744 Planarity : 0.004 0.052 6196 Dihedral : 15.239 173.323 6013 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 2.21 % Allowed : 15.64 % Favored : 82.15 % 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: -0.91 (0.13), residues: 4293 helix: 0.77 (0.14), residues: 1532 sheet: -1.20 (0.21), residues: 597 loop : -1.44 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 779 TYR 0.030 0.001 TYR H 177 PHE 0.011 0.001 PHE J 892 TRP 0.010 0.001 TRP I 183 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00310 (36896) covalent geometry : angle 0.55113 (50385) hydrogen bonds : bond 0.03542 ( 1437) hydrogen bonds : angle 4.11450 ( 3914) metal coordination : bond 0.00945 ( 8) metal coordination : angle 5.14227 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 393 time to evaluate : 1.109 Fit side-chains REVERT: A 157 MET cc_start: 0.7479 (mmt) cc_final: 0.7217 (mmp) REVERT: A 298 ASP cc_start: 0.8901 (t70) cc_final: 0.8565 (t0) REVERT: A 740 GLU cc_start: 0.8387 (mp0) cc_final: 0.7997 (mp0) REVERT: A 1026 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: A 1067 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7886 (tmm-80) REVERT: G 10 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8398 (mmtm) REVERT: G 29 GLU cc_start: 0.9027 (tt0) cc_final: 0.8686 (pt0) REVERT: G 62 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: G 141 SER cc_start: 0.8893 (p) cc_final: 0.8472 (p) REVERT: H 127 GLN cc_start: 0.9228 (pm20) cc_final: 0.9013 (mp10) REVERT: H 199 ASP cc_start: 0.8398 (m-30) cc_final: 0.7946 (t0) REVERT: I 18 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.8257 (mmt-90) REVERT: I 69 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8755 (pt0) REVERT: I 81 ASP cc_start: 0.8554 (p0) cc_final: 0.7736 (p0) REVERT: I 84 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: I 85 CYS cc_start: 0.8978 (m) cc_final: 0.8510 (m) REVERT: I 239 MET cc_start: 0.5020 (tmm) cc_final: 0.4796 (tmm) REVERT: I 337 PHE cc_start: 0.8559 (t80) cc_final: 0.8082 (t80) REVERT: I 351 LEU cc_start: 0.8295 (mt) cc_final: 0.8017 (mt) REVERT: I 410 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8659 (mm) REVERT: I 422 LYS cc_start: 0.7639 (mppt) cc_final: 0.7328 (ttpp) REVERT: I 483 ASP cc_start: 0.8309 (t70) cc_final: 0.7873 (t70) REVERT: I 618 GLN cc_start: 0.7677 (tt0) cc_final: 0.7388 (tt0) REVERT: I 1034 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7833 (mmm-85) REVERT: I 1096 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8701 (mt) REVERT: I 1297 ASP cc_start: 0.8605 (t70) cc_final: 0.8350 (t0) REVERT: J 129 ASP cc_start: 0.8274 (t0) cc_final: 0.7687 (t0) REVERT: J 229 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: J 289 ASP cc_start: 0.8304 (m-30) cc_final: 0.7815 (t0) REVERT: J 294 ASN cc_start: 0.8127 (m-40) cc_final: 0.7564 (m110) REVERT: J 295 GLU cc_start: 0.8633 (tp30) cc_final: 0.8096 (tp30) REVERT: J 837 ASP cc_start: 0.9062 (m-30) cc_final: 0.8518 (t0) REVERT: J 844 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8107 (p) REVERT: J 997 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7472 (m) REVERT: J 1165 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6782 (m-10) REVERT: J 1189 MET cc_start: 0.7161 (mmm) cc_final: 0.6942 (mmm) REVERT: J 1261 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8253 (pp) REVERT: J 1334 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8368 (tp30) outliers start: 80 outliers final: 64 residues processed: 456 average time/residue: 0.2359 time to fit residues: 173.8968 Evaluate side-chains 460 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 385 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Chi-restraints excluded: chain J residue 1326 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 137 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 387 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 425 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN I1061 GLN ** J 865 HIS ** 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 = 0.3903 r_free = 0.3903 target = 0.154921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107532 restraints weight = 48527.397| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.32 r_work: 0.3121 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36904 Z= 0.138 Angle : 0.557 15.337 50397 Z= 0.287 Chirality : 0.042 0.213 5744 Planarity : 0.004 0.050 6196 Dihedral : 15.210 173.337 6013 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 2.18 % Allowed : 15.99 % Favored : 81.82 % 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: -0.85 (0.13), residues: 4293 helix: 0.82 (0.14), residues: 1529 sheet: -1.17 (0.21), residues: 598 loop : -1.41 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 779 TYR 0.036 0.001 TYR H 177 PHE 0.028 0.001 PHE A 972 TRP 0.010 0.001 TRP I 183 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00322 (36896) covalent geometry : angle 0.55111 (50385) hydrogen bonds : bond 0.03532 ( 1437) hydrogen bonds : angle 4.08815 ( 3914) metal coordination : bond 0.00958 ( 8) metal coordination : angle 5.16716 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10858.30 seconds wall clock time: 185 minutes 48.37 seconds (11148.37 seconds total)