Starting phenix.real_space_refine on Fri Aug 7 00:43:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1y_61984/08_2026/9k1y_61984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1y_61984/08_2026/9k1y_61984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k1y_61984/08_2026/9k1y_61984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1y_61984/08_2026/9k1y_61984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k1y_61984/08_2026/9k1y_61984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1y_61984/08_2026/9k1y_61984.map" } resolution = 3.1 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 38 5.49 5 S 102 5.16 5 C 11151 2.51 5 N 3042 2.21 5 O 3407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17743 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6421 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 34, 'TRANS': 773} Chain: "D" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "A" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9139 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 60, 'TRANS': 1104} Chain breaks: 5 Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 584 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 505 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 19} Chain: "H" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6590 SG CYS D 23 86.098 61.846 42.655 1.00 34.70 S ATOM 6614 SG CYS D 26 83.854 58.947 43.343 1.00 35.58 S ATOM 6861 SG CYS D 58 85.384 61.051 46.210 1.00 32.20 S ATOM 6882 SG CYS D 61 87.649 58.759 44.153 1.00 34.61 S ATOM 6503 SG CYS D 11 86.818 55.494 60.374 1.00 29.44 S ATOM 6766 SG CYS D 46 86.482 59.170 61.799 1.00 31.21 S ATOM 6789 SG CYS D 49 87.574 58.682 58.376 1.00 36.31 S ATOM 7060 SG CYS D 85 83.921 57.489 59.576 1.00 26.39 S ATOM 6641 SG CYS D 30 73.070 57.438 49.178 1.00 28.76 S ATOM 6662 SG CYS D 33 71.849 54.251 47.591 1.00 29.77 S ATOM 6957 SG CYS D 72 69.301 56.802 48.657 1.00 26.68 S ATOM 6981 SG CYS D 75 71.058 54.908 51.308 1.00 22.69 S Time building chain proxies: 3.81, per 1000 atoms: 0.21 Number of scatterers: 17743 At special positions: 0 Unit cell: (134.2, 134.2, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 102 16.00 P 38 15.00 O 3407 8.00 N 3042 7.00 C 11151 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: 1.55 Conformation dependent library (CDL) restraints added in 774.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 26 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 49 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " Number of angles added : 18 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4022 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 27 sheets defined 41.4% alpha, 19.0% beta 13 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'C' and resid 497 through 506 Processing helix chain 'C' and resid 508 through 527 removed outlier: 4.094A pdb=" N ALA C 523 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU C 525 " --> pdb=" O ASP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 540 removed outlier: 3.848A pdb=" N LEU C 531 " --> pdb=" O GLY C 527 " (cutoff:3.500A) Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 563 removed outlier: 3.686A pdb=" N ARG C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 removed outlier: 3.610A pdb=" N VAL C 567 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Proline residue: C 569 - end of helix Processing helix chain 'C' and resid 570 through 579 Processing helix chain 'C' and resid 580 through 583 Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 621 through 638 removed outlier: 3.699A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 643 removed outlier: 3.511A pdb=" N SER C 643 " --> pdb=" O GLY C 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 640 through 643' Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.859A pdb=" N LYS C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 676 removed outlier: 4.088A pdb=" N ARG C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 676 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 681 removed outlier: 3.686A pdb=" N LEU C 680 " --> pdb=" O CYS C 677 " (cutoff:3.500A) Proline residue: C 681 - end of helix No H-bonds generated for 'chain 'C' and resid 677 through 681' Processing helix chain 'C' and resid 682 through 695 removed outlier: 3.867A pdb=" N LEU C 686 " --> pdb=" O HIS C 682 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 716 Processing helix chain 'C' and resid 727 through 738 removed outlier: 4.341A pdb=" N ARG C 736 " --> pdb=" O TRP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 777 removed outlier: 4.487A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 797 Processing helix chain 'C' and resid 802 through 810 Processing helix chain 'C' and resid 810 through 819 removed outlier: 3.505A pdb=" N TRP C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 825 removed outlier: 3.631A pdb=" N ALA C 824 " --> pdb=" O HIS C 821 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 825 " --> pdb=" O ARG C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 825' Processing helix chain 'C' and resid 826 through 845 Processing helix chain 'C' and resid 845 through 854 removed outlier: 3.934A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 879 removed outlier: 3.604A pdb=" N ARG C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 902 removed outlier: 3.728A pdb=" N GLU C 902 " --> pdb=" O TYR C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 922 removed outlier: 4.047A pdb=" N LEU C 911 " --> pdb=" O ASP C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 927 Proline residue: C 927 - end of helix Processing helix chain 'C' and resid 928 through 941 Processing helix chain 'C' and resid 942 through 946 removed outlier: 3.888A pdb=" N ALA C 945 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 946 " --> pdb=" O LYS C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 942 through 946' Processing helix chain 'C' and resid 947 through 965 removed outlier: 5.145A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.594A pdb=" N MET C 971 " --> pdb=" O GLU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 986 through 1004 Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1028 through 1046 removed outlier: 3.674A pdb=" N ASN C1034 " --> pdb=" O LYS C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1050 removed outlier: 3.844A pdb=" N VAL C1050 " --> pdb=" O ALA C1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1047 through 1050' Processing helix chain 'C' and resid 1051 through 1066 Processing helix chain 'C' and resid 1070 through 1088 removed outlier: 3.685A pdb=" N ARG C1074 " --> pdb=" O LYS C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1099 Processing helix chain 'C' and resid 1105 through 1123 Processing helix chain 'C' and resid 1124 through 1136 removed outlier: 4.124A pdb=" N VAL C1128 " --> pdb=" O SER C1124 " (cutoff:3.500A) Proline residue: C1130 - end of helix Processing helix chain 'C' and resid 1140 through 1158 removed outlier: 3.615A pdb=" N GLN C1144 " --> pdb=" O GLU C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1164 No H-bonds generated for 'chain 'C' and resid 1162 through 1164' Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 3.628A pdb=" N VAL C1169 " --> pdb=" O TYR C1165 " (cutoff:3.500A) Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.709A pdb=" N ARG C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.626A pdb=" N LEU C1208 " --> pdb=" O CYS C1204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS C1210 " --> pdb=" O ASP C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1219 No H-bonds generated for 'chain 'C' and resid 1217 through 1219' Processing helix chain 'C' and resid 1223 through 1242 Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.937A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1275 removed outlier: 3.596A pdb=" N ARG C1262 " --> pdb=" O ALA C1258 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP C1263 " --> pdb=" O ARG C1259 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1283 removed outlier: 3.692A pdb=" N LEU C1280 " --> pdb=" O SER C1276 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C1282 " --> pdb=" O ASP C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1302 removed outlier: 3.515A pdb=" N TYR C1302 " --> pdb=" O GLU C1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.171A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.850A pdb=" N ASP A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 808 through 826 Processing helix chain 'A' and resid 837 through 845 removed outlier: 4.062A pdb=" N ALA A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 1134 through 1152 Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1176 through 1181 Processing helix chain 'A' and resid 1182 through 1185 Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.957A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 removed outlier: 3.558A pdb=" N LYS B 17 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.531A pdb=" N TRP B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 57 removed outlier: 3.571A pdb=" N GLU B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 73 removed outlier: 4.248A pdb=" N LEU B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 19 removed outlier: 4.271A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.101A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 3.737A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 3 " --> pdb=" O ILE A1174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.806A pdb=" N LEU A 38 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 55 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 40 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.635A pdb=" N PHE A 68 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 87 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 104 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 89 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 98 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA8, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA9, first strand: chain 'A' and resid 165 through 173 removed outlier: 5.437A pdb=" N VAL A 167 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS A 169 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 234 through 237 removed outlier: 4.196A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.780A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 287 through 292 removed outlier: 6.903A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR A 314 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 327 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU A 316 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE A 325 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.835A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.538A pdb=" N TYR A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AB7, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AB8, first strand: chain 'A' and resid 516 through 520 removed outlier: 3.787A pdb=" N LEU A 516 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 524 " --> pdb=" O TRP A 536 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 536 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 544 through 549 removed outlier: 3.861A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 566 through 568 Processing sheet with id=AC2, first strand: chain 'A' and resid 587 through 591 removed outlier: 3.794A pdb=" N CYS A 589 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 591 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 606 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 605 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 609 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AC4, first strand: chain 'A' and resid 702 through 706 removed outlier: 6.596A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N SER A 724 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 721 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A 732 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 723 " --> pdb=" O HIS A 730 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 785 through 791 removed outlier: 6.298A pdb=" N THR A 802 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 787 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 796 " --> pdb=" O HIS A 791 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER A 864 " --> pdb=" O GLN A 881 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLN A 881 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 866 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 879 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 868 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 886 through 894 removed outlier: 6.140A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 891 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 906 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 893 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 904 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 905 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS A 941 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 953 through 955 removed outlier: 3.583A pdb=" N VAL A 959 " --> pdb=" O TYR A 970 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 969 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 990 through 996 removed outlier: 3.509A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A1087 " --> pdb=" O PHE A1024 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 6.354A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5673 1.34 - 1.46: 3171 1.46 - 1.58: 9096 1.58 - 1.70: 74 1.70 - 1.82: 157 Bond restraints: 18171 Sorted by residual: bond pdb=" N1 C H 10 " pdb=" C2 C H 10 " ideal model delta sigma weight residual 1.397 1.408 -0.011 1.00e-02 1.00e+04 1.13e+00 bond pdb=" N ASP A 367 " pdb=" CA ASP A 367 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" CA GLU C 595 " pdb=" CB GLU C 595 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.74e-02 3.30e+03 1.06e+00 bond pdb=" C ARG C 767 " pdb=" O ARG C 767 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.19e-02 7.06e+03 1.03e+00 bond pdb=" CD GLU C 595 " pdb=" OE1 GLU C 595 " ideal model delta sigma weight residual 1.249 1.231 0.018 1.90e-02 2.77e+03 9.17e-01 ... (remaining 18166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 23998 1.35 - 2.70: 628 2.70 - 4.05: 122 4.05 - 5.40: 32 5.40 - 6.75: 15 Bond angle restraints: 24795 Sorted by residual: angle pdb=" N SER A 717 " pdb=" CA SER A 717 " pdb=" C SER A 717 " ideal model delta sigma weight residual 114.56 108.32 6.24 1.27e+00 6.20e-01 2.41e+01 angle pdb=" O5' U H 4 " pdb=" C5' U H 4 " pdb=" C4' U H 4 " ideal model delta sigma weight residual 109.40 112.79 -3.39 8.00e-01 1.56e+00 1.79e+01 angle pdb=" C1' C H 10 " pdb=" N1 C H 10 " pdb=" C2 C H 10 " ideal model delta sigma weight residual 118.80 123.25 -4.45 1.10e+00 8.26e-01 1.63e+01 angle pdb=" N GLU C 595 " pdb=" CA GLU C 595 " pdb=" CB GLU C 595 " ideal model delta sigma weight residual 110.39 116.98 -6.59 1.66e+00 3.63e-01 1.58e+01 angle pdb=" O5' U G 42 " pdb=" C5' U G 42 " pdb=" C4' U G 42 " ideal model delta sigma weight residual 109.40 112.27 -2.87 8.00e-01 1.56e+00 1.29e+01 ... (remaining 24790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.76: 9944 19.76 - 39.51: 873 39.51 - 59.27: 176 59.27 - 79.02: 50 79.02 - 98.78: 14 Dihedral angle restraints: 11057 sinusoidal: 4815 harmonic: 6242 Sorted by residual: dihedral pdb=" CA GLU A 136 " pdb=" C GLU A 136 " pdb=" N LYS A 137 " pdb=" CA LYS A 137 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LYS C 943 " pdb=" C LYS C 943 " pdb=" N SER C 944 " pdb=" CA SER C 944 " ideal model delta harmonic sigma weight residual 180.00 161.02 18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLU C 545 " pdb=" C GLU C 545 " pdb=" N ASP C 546 " pdb=" CA ASP C 546 " ideal model delta harmonic sigma weight residual 180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 11054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1899 0.035 - 0.069: 605 0.069 - 0.104: 223 0.104 - 0.138: 116 0.138 - 0.173: 6 Chirality restraints: 2849 Sorted by residual: chirality pdb=" C1' U G 34 " pdb=" O4' U G 34 " pdb=" C2' U G 34 " pdb=" N1 U G 34 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA LYS C 943 " pdb=" N LYS C 943 " pdb=" C LYS C 943 " pdb=" CB LYS C 943 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA THR C 717 " pdb=" N THR C 717 " pdb=" C THR C 717 " pdb=" CB THR C 717 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 2846 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G H 3 " -0.031 2.00e-02 2.50e+03 1.45e-02 6.30e+00 pdb=" N9 G H 3 " 0.038 2.00e-02 2.50e+03 pdb=" C8 G H 3 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G H 3 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G H 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G H 3 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G H 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G H 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G H 3 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G H 3 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G H 3 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G H 3 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 34 " -0.022 2.00e-02 2.50e+03 1.21e-02 3.31e+00 pdb=" N1 U G 34 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U G 34 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U G 34 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U G 34 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U G 34 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U G 34 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U G 34 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U G 34 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 680 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 681 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.021 5.00e-02 4.00e+02 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3392 2.78 - 3.31: 16629 3.31 - 3.84: 28875 3.84 - 4.37: 33413 4.37 - 4.90: 57437 Nonbonded interactions: 139746 Sorted by model distance: nonbonded pdb=" O SER A 246 " pdb=" OH TYR A 258 " model vdw 2.249 3.040 nonbonded pdb=" OG SER A 629 " pdb=" O PRO A 681 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A1008 " pdb=" O TYR A1029 " model vdw 2.265 3.040 nonbonded pdb=" O ILE C1166 " pdb=" OG1 THR C1170 " model vdw 2.268 3.040 nonbonded pdb=" O GLU C 776 " pdb=" OG SER C 779 " model vdw 2.285 3.040 ... (remaining 139741 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.002 0.046 18183 Z= 0.120 Angle : 0.575 9.732 24813 Z= 0.331 Chirality : 0.044 0.173 2849 Planarity : 0.004 0.038 3058 Dihedral : 15.805 98.776 7035 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.18), residues: 2129 helix: 1.54 (0.19), residues: 761 sheet: -0.79 (0.25), residues: 435 loop : -1.32 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1057 TYR 0.017 0.001 TYR C 979 PHE 0.014 0.001 PHE A 955 TRP 0.009 0.001 TRP C 732 HIS 0.006 0.001 HIS A1143 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (18171) covalent geometry : angle 0.56332 / 0.33 (24795) hydrogen bonds : bond 0.17157 / 11.56 ( 786) hydrogen bonds : angle 6.67889 / 4.97 ( 2213) metal coordination : bond 0.00405 / 0.23 ( 12) metal coordination : angle 4.39916 / 2.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: C 1135 GLU cc_start: 0.7603 (tp30) cc_final: 0.7346 (tp30) REVERT: C 1246 MET cc_start: 0.7619 (mmm) cc_final: 0.7307 (mmm) REVERT: A 393 LYS cc_start: 0.7047 (ttpt) cc_final: 0.6836 (tttt) REVERT: A 1023 ILE cc_start: 0.7250 (pt) cc_final: 0.7037 (pt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1585 time to fit residues: 49.4511 Evaluate side-chains 174 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 949 GLN C1142 ASN A1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.150645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112242 restraints weight = 29534.949| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.05 r_work: 0.3281 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18183 Z= 0.183 Angle : 0.632 11.490 24813 Z= 0.328 Chirality : 0.046 0.263 2849 Planarity : 0.005 0.042 3058 Dihedral : 11.875 94.571 2912 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.81 % Allowed : 7.44 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.18), residues: 2129 helix: 1.45 (0.19), residues: 765 sheet: -0.80 (0.24), residues: 473 loop : -1.39 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 524 TYR 0.017 0.002 TYR C 805 PHE 0.022 0.002 PHE A 234 TRP 0.012 0.002 TRP B 29 HIS 0.008 0.001 HIS A1143 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (18171) covalent geometry : angle 0.61804 / 0.33 (24795) hydrogen bonds : bond 0.05566 / 3.74 ( 786) hydrogen bonds : angle 5.28500 / 3.91 ( 2213) metal coordination : bond 0.00574 / 0.39 ( 12) metal coordination : angle 5.02138 / 3.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: C 1246 MET cc_start: 0.8112 (mmm) cc_final: 0.7763 (mmm) REVERT: D 12 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.7936 (ptp-110) REVERT: D 83 ASP cc_start: 0.8299 (t0) cc_final: 0.8095 (t0) REVERT: A 55 THR cc_start: 0.8926 (m) cc_final: 0.8656 (m) REVERT: A 393 LYS cc_start: 0.7458 (ttpt) cc_final: 0.7148 (tttt) REVERT: A 815 ARG cc_start: 0.7611 (mmm160) cc_final: 0.6917 (ttt90) REVERT: A 1023 ILE cc_start: 0.7433 (pt) cc_final: 0.7115 (pt) outliers start: 15 outliers final: 9 residues processed: 193 average time/residue: 0.1573 time to fit residues: 45.7332 Evaluate side-chains 179 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 71 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 666 ASN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.149847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108918 restraints weight = 29721.080| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.75 r_work: 0.3242 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18183 Z= 0.145 Angle : 0.584 9.284 24813 Z= 0.303 Chirality : 0.044 0.332 2849 Planarity : 0.004 0.039 3058 Dihedral : 11.850 97.825 2912 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.19 % Allowed : 10.29 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.18), residues: 2129 helix: 1.42 (0.19), residues: 762 sheet: -0.72 (0.24), residues: 470 loop : -1.38 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1057 TYR 0.016 0.001 TYR C 805 PHE 0.016 0.001 PHE A 234 TRP 0.011 0.001 TRP B 29 HIS 0.005 0.001 HIS A1143 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (18171) covalent geometry : angle 0.57094 / 0.30 (24795) hydrogen bonds : bond 0.05127 / 3.46 ( 786) hydrogen bonds : angle 5.01606 / 3.69 ( 2213) metal coordination : bond 0.00514 / 0.33 ( 12) metal coordination : angle 4.67745 / 3.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: C 1057 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.7258 (mtm180) REVERT: C 1246 MET cc_start: 0.8165 (mmm) cc_final: 0.7814 (mmm) REVERT: D 12 ARG cc_start: 0.8490 (ptp-110) cc_final: 0.8010 (ptp-110) REVERT: D 83 ASP cc_start: 0.8318 (t0) cc_final: 0.8001 (t0) REVERT: A 393 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6869 (tttt) REVERT: A 706 MET cc_start: 0.3792 (mpp) cc_final: 0.3058 (ttt) REVERT: A 815 ARG cc_start: 0.7527 (mmm160) cc_final: 0.6872 (ttt90) REVERT: A 1023 ILE cc_start: 0.7476 (pt) cc_final: 0.7163 (pt) outliers start: 22 outliers final: 15 residues processed: 196 average time/residue: 0.1498 time to fit residues: 43.8015 Evaluate side-chains 186 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 45 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 180 optimal weight: 0.0370 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.149884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108982 restraints weight = 29253.447| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.65 r_work: 0.3246 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18183 Z= 0.144 Angle : 0.579 10.173 24813 Z= 0.299 Chirality : 0.044 0.383 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.839 99.677 2912 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.51 % Allowed : 11.64 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.18), residues: 2129 helix: 1.42 (0.19), residues: 765 sheet: -0.70 (0.24), residues: 469 loop : -1.40 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1057 TYR 0.019 0.001 TYR C 805 PHE 0.016 0.001 PHE A 234 TRP 0.012 0.002 TRP C 732 HIS 0.009 0.001 HIS C 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (18171) covalent geometry : angle 0.56688 / 0.30 (24795) hydrogen bonds : bond 0.04906 / 3.31 ( 786) hydrogen bonds : angle 4.85910 / 3.56 ( 2213) metal coordination : bond 0.00507 / 0.33 ( 12) metal coordination : angle 4.45599 / 2.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7846 (mp0) cc_final: 0.7343 (mp0) REVERT: C 898 TYR cc_start: 0.7812 (t80) cc_final: 0.7473 (t80) REVERT: C 1056 MET cc_start: 0.7900 (mmm) cc_final: 0.7564 (mmt) REVERT: C 1246 MET cc_start: 0.8144 (mmm) cc_final: 0.7814 (mmm) REVERT: D 12 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.7896 (ptp-110) REVERT: D 83 ASP cc_start: 0.8311 (t0) cc_final: 0.7994 (t0) REVERT: A 55 THR cc_start: 0.8958 (m) cc_final: 0.8706 (m) REVERT: A 393 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6849 (tttt) REVERT: A 706 MET cc_start: 0.3815 (mpp) cc_final: 0.2966 (ttt) REVERT: A 712 VAL cc_start: 0.2542 (OUTLIER) cc_final: 0.2281 (p) REVERT: A 815 ARG cc_start: 0.7540 (mmm160) cc_final: 0.6910 (ttt180) REVERT: A 1023 ILE cc_start: 0.7468 (pt) cc_final: 0.7145 (pt) REVERT: B 72 MET cc_start: 0.8426 (mmm) cc_final: 0.8131 (tpp) outliers start: 28 outliers final: 22 residues processed: 197 average time/residue: 0.1448 time to fit residues: 42.8801 Evaluate side-chains 193 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 941 HIS A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.150292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109455 restraints weight = 29310.055| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.82 r_work: 0.3255 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18183 Z= 0.126 Angle : 0.558 13.139 24813 Z= 0.287 Chirality : 0.043 0.441 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.812 101.196 2912 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.51 % Allowed : 12.34 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.18), residues: 2129 helix: 1.45 (0.19), residues: 765 sheet: -0.64 (0.24), residues: 464 loop : -1.40 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 524 TYR 0.020 0.001 TYR C 805 PHE 0.014 0.001 PHE A 234 TRP 0.012 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (18171) covalent geometry : angle 0.54627 / 0.29 (24795) hydrogen bonds : bond 0.04560 / 3.08 ( 786) hydrogen bonds : angle 4.73891 / 3.46 ( 2213) metal coordination : bond 0.00445 / 0.29 ( 12) metal coordination : angle 4.19774 / 2.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7819 (mp0) cc_final: 0.7264 (mp0) REVERT: C 1246 MET cc_start: 0.8055 (mmm) cc_final: 0.7739 (mmm) REVERT: D 12 ARG cc_start: 0.8389 (ptp-110) cc_final: 0.7824 (ptp-110) REVERT: D 83 ASP cc_start: 0.8321 (t0) cc_final: 0.7949 (t0) REVERT: A 55 THR cc_start: 0.8975 (m) cc_final: 0.8700 (m) REVERT: A 393 LYS cc_start: 0.7233 (ttpt) cc_final: 0.6827 (tttt) REVERT: A 706 MET cc_start: 0.3918 (mpp) cc_final: 0.3109 (ttt) REVERT: A 712 VAL cc_start: 0.2656 (OUTLIER) cc_final: 0.2412 (p) REVERT: A 815 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6924 (ttt180) REVERT: A 1023 ILE cc_start: 0.7420 (pt) cc_final: 0.7112 (pt) REVERT: A 1191 LYS cc_start: 0.7936 (mttt) cc_final: 0.7478 (mmtt) REVERT: B 14 LEU cc_start: 0.6832 (tp) cc_final: 0.6552 (tp) REVERT: B 72 MET cc_start: 0.8347 (mmm) cc_final: 0.8046 (tpp) outliers start: 28 outliers final: 22 residues processed: 194 average time/residue: 0.1417 time to fit residues: 41.5507 Evaluate side-chains 191 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 878 ASN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.149581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109451 restraints weight = 29061.194| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.52 r_work: 0.3263 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18183 Z= 0.146 Angle : 0.567 8.689 24813 Z= 0.294 Chirality : 0.043 0.169 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.817 101.738 2912 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.26 % Allowed : 12.93 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.18), residues: 2129 helix: 1.44 (0.19), residues: 771 sheet: -0.59 (0.24), residues: 457 loop : -1.46 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1199 TYR 0.021 0.001 TYR C 805 PHE 0.017 0.001 PHE A 234 TRP 0.013 0.001 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (18171) covalent geometry : angle 0.55472 / 0.29 (24795) hydrogen bonds : bond 0.04802 / 3.25 ( 786) hydrogen bonds : angle 4.71838 / 3.44 ( 2213) metal coordination : bond 0.00496 / 0.33 ( 12) metal coordination : angle 4.35160 / 2.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7823 (mp0) cc_final: 0.7245 (mp0) REVERT: C 898 TYR cc_start: 0.7754 (t80) cc_final: 0.7482 (t80) REVERT: C 1056 MET cc_start: 0.7806 (mmm) cc_final: 0.7482 (mmt) REVERT: D 83 ASP cc_start: 0.8301 (t0) cc_final: 0.7907 (t0) REVERT: A 55 THR cc_start: 0.8969 (m) cc_final: 0.8674 (m) REVERT: A 393 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6774 (tttt) REVERT: A 815 ARG cc_start: 0.7549 (mmm160) cc_final: 0.6892 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7410 (pt) cc_final: 0.7108 (pt) REVERT: A 1191 LYS cc_start: 0.7974 (mttt) cc_final: 0.7537 (mmtt) REVERT: B 14 LEU cc_start: 0.6905 (tp) cc_final: 0.6649 (tp) REVERT: B 72 MET cc_start: 0.8355 (mmm) cc_final: 0.8071 (tpp) outliers start: 42 outliers final: 32 residues processed: 205 average time/residue: 0.1256 time to fit residues: 38.8592 Evaluate side-chains 200 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 77 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 878 ASN A1017 ASN B 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.149453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109351 restraints weight = 29517.735| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.54 r_work: 0.3243 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18183 Z= 0.153 Angle : 0.589 10.428 24813 Z= 0.302 Chirality : 0.044 0.268 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.828 102.294 2912 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.89 % Allowed : 13.31 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.18), residues: 2129 helix: 1.41 (0.19), residues: 771 sheet: -0.60 (0.24), residues: 457 loop : -1.49 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1199 TYR 0.021 0.001 TYR C 805 PHE 0.017 0.001 PHE A 234 TRP 0.014 0.002 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (18171) covalent geometry : angle 0.57290 / 0.30 (24795) hydrogen bonds : bond 0.04891 / 3.30 ( 786) hydrogen bonds : angle 4.72962 / 3.44 ( 2213) metal coordination : bond 0.00553 / 0.36 ( 12) metal coordination : angle 5.06135 / 3.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7819 (mp0) cc_final: 0.7217 (mp0) REVERT: C 898 TYR cc_start: 0.7887 (t80) cc_final: 0.7519 (t80) REVERT: C 1056 MET cc_start: 0.7852 (mmm) cc_final: 0.7494 (mmt) REVERT: D 83 ASP cc_start: 0.8329 (t0) cc_final: 0.7898 (t0) REVERT: A 55 THR cc_start: 0.8986 (m) cc_final: 0.8637 (m) REVERT: A 393 LYS cc_start: 0.7363 (ttpt) cc_final: 0.6914 (tttt) REVERT: A 706 MET cc_start: 0.3847 (mpp) cc_final: 0.2717 (ttt) REVERT: A 815 ARG cc_start: 0.7514 (mmm160) cc_final: 0.6839 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7453 (pt) cc_final: 0.7156 (pt) REVERT: A 1191 LYS cc_start: 0.7944 (mttt) cc_final: 0.7525 (mmtt) REVERT: B 14 LEU cc_start: 0.6941 (tp) cc_final: 0.6647 (tp) REVERT: B 72 MET cc_start: 0.8389 (mmm) cc_final: 0.8093 (tpp) outliers start: 35 outliers final: 30 residues processed: 193 average time/residue: 0.1406 time to fit residues: 41.1134 Evaluate side-chains 197 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 202 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 878 ASN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109166 restraints weight = 29168.116| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.89 r_work: 0.3266 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18183 Z= 0.122 Angle : 0.555 8.627 24813 Z= 0.286 Chirality : 0.042 0.171 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.787 103.125 2912 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.94 % Allowed : 13.74 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.18), residues: 2129 helix: 1.47 (0.19), residues: 772 sheet: -0.51 (0.25), residues: 449 loop : -1.45 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1199 TYR 0.021 0.001 TYR C 805 PHE 0.016 0.001 PHE C1126 TRP 0.013 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (18171) covalent geometry : angle 0.54146 / 0.29 (24795) hydrogen bonds : bond 0.04356 / 2.95 ( 786) hydrogen bonds : angle 4.60905 / 3.35 ( 2213) metal coordination : bond 0.00442 / 0.28 ( 12) metal coordination : angle 4.49603 / 2.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: D 83 ASP cc_start: 0.8366 (t0) cc_final: 0.7965 (t0) REVERT: A 55 THR cc_start: 0.8912 (m) cc_final: 0.8631 (p) REVERT: A 393 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7169 (tttt) REVERT: A 583 MET cc_start: 0.3250 (tpp) cc_final: 0.2408 (mmm) REVERT: A 706 MET cc_start: 0.4013 (mpp) cc_final: 0.2719 (ttt) REVERT: A 815 ARG cc_start: 0.7510 (mmm160) cc_final: 0.6815 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7431 (pt) cc_final: 0.7134 (pt) REVERT: A 1191 LYS cc_start: 0.7938 (mttt) cc_final: 0.7474 (mmtt) REVERT: B 72 MET cc_start: 0.8353 (mmm) cc_final: 0.8033 (tpp) outliers start: 36 outliers final: 28 residues processed: 201 average time/residue: 0.1312 time to fit residues: 40.1433 Evaluate side-chains 197 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 153 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 chunk 4 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 886 HIS A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.151816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111115 restraints weight = 29278.743| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.96 r_work: 0.3282 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18183 Z= 0.103 Angle : 0.536 10.117 24813 Z= 0.276 Chirality : 0.042 0.165 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.705 103.559 2912 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.40 % Allowed : 14.76 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.18), residues: 2129 helix: 1.58 (0.19), residues: 772 sheet: -0.34 (0.25), residues: 442 loop : -1.41 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.018 0.001 TYR C 979 PHE 0.014 0.001 PHE C1126 TRP 0.011 0.001 TRP C1055 HIS 0.003 0.001 HIS C 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (18171) covalent geometry : angle 0.52591 / 0.28 (24795) hydrogen bonds : bond 0.03768 / 2.56 ( 786) hydrogen bonds : angle 4.46348 / 3.25 ( 2213) metal coordination : bond 0.00337 / 0.20 ( 12) metal coordination : angle 3.81032 / 2.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7827 (mp0) cc_final: 0.7278 (mp0) REVERT: C 1006 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6812 (mtm) REVERT: D 83 ASP cc_start: 0.8278 (t0) cc_final: 0.7942 (t0) REVERT: A 55 THR cc_start: 0.8902 (m) cc_final: 0.8617 (p) REVERT: A 393 LYS cc_start: 0.7248 (ttpt) cc_final: 0.7014 (tttt) REVERT: A 706 MET cc_start: 0.3876 (mpp) cc_final: 0.2860 (ttt) REVERT: A 815 ARG cc_start: 0.7502 (mmm160) cc_final: 0.6803 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7387 (pt) cc_final: 0.7093 (pt) REVERT: A 1191 LYS cc_start: 0.7946 (mttt) cc_final: 0.7493 (mmtt) outliers start: 26 outliers final: 21 residues processed: 196 average time/residue: 0.1268 time to fit residues: 37.7192 Evaluate side-chains 193 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109734 restraints weight = 29234.528| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.65 r_work: 0.3253 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18183 Z= 0.131 Angle : 0.566 8.805 24813 Z= 0.290 Chirality : 0.043 0.167 2849 Planarity : 0.004 0.037 3058 Dihedral : 11.706 102.717 2912 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.45 % Allowed : 15.03 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.18), residues: 2129 helix: 1.52 (0.19), residues: 772 sheet: -0.41 (0.25), residues: 449 loop : -1.42 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 775 TYR 0.014 0.001 TYR C 979 PHE 0.016 0.001 PHE A 788 TRP 0.018 0.001 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (18171) covalent geometry : angle 0.55401 / 0.29 (24795) hydrogen bonds : bond 0.04369 / 2.97 ( 786) hydrogen bonds : angle 4.52916 / 3.30 ( 2213) metal coordination : bond 0.00433 / 0.28 ( 12) metal coordination : angle 4.36182 / 2.83 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1006 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6859 (mtm) REVERT: D 83 ASP cc_start: 0.8283 (t0) cc_final: 0.7962 (t0) REVERT: A 55 THR cc_start: 0.8947 (m) cc_final: 0.8670 (p) REVERT: A 393 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6805 (tttt) REVERT: A 706 MET cc_start: 0.3933 (mpp) cc_final: 0.2796 (ttt) REVERT: A 815 ARG cc_start: 0.7562 (mmm160) cc_final: 0.6857 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7401 (pt) cc_final: 0.7094 (pt) REVERT: A 1191 LYS cc_start: 0.7951 (mttt) cc_final: 0.7510 (mmtt) outliers start: 27 outliers final: 23 residues processed: 187 average time/residue: 0.1227 time to fit residues: 34.9983 Evaluate side-chains 190 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 777 PHE Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 67 optimal weight: 0.0050 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109641 restraints weight = 29472.292| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.85 r_work: 0.3240 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18183 Z= 0.126 Angle : 0.565 8.527 24813 Z= 0.289 Chirality : 0.043 0.169 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.700 103.002 2912 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.40 % Allowed : 15.14 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.18), residues: 2129 helix: 1.51 (0.19), residues: 772 sheet: -0.40 (0.25), residues: 452 loop : -1.45 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 775 TYR 0.015 0.001 TYR C 979 PHE 0.014 0.001 PHE A 234 TRP 0.020 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (18171) covalent geometry : angle 0.55235 / 0.29 (24795) hydrogen bonds : bond 0.04311 / 2.93 ( 786) hydrogen bonds : angle 4.51839 / 3.29 ( 2213) metal coordination : bond 0.00432 / 0.28 ( 12) metal coordination : angle 4.36814 / 2.82 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4947.18 seconds wall clock time: 85 minutes 13.05 seconds (5113.05 seconds total)