Starting phenix.real_space_refine on Sat Jul 4 04:26:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1y_61984/07_2026/9k1y_61984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1y_61984/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1y_61984/07_2026/9k1y_61984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1y_61984/07_2026/9k1y_61984.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1y_61984/07_2026/9k1y_61984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1y_61984/07_2026/9k1y_61984.cif" } 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-dev-6108/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: 4.67, per 1000 atoms: 0.26 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: 1.63 Conformation dependent library (CDL) restraints added in 874.2 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: 2.03 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: 3.46 Time building geometry restraints manager: 2.11 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: 24104 1.35 - 2.70: 533 2.70 - 4.05: 111 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=" 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=" C ARG C 594 " pdb=" N GLU C 595 " pdb=" CA GLU C 595 " ideal model delta sigma weight residual 120.72 115.00 5.72 1.67e+00 3.59e-01 1.17e+01 angle pdb=" N GLU C 980 " pdb=" CA GLU C 980 " pdb=" CB GLU C 980 " ideal model delta sigma weight residual 110.39 115.96 -5.57 1.66e+00 3.63e-01 1.13e+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 - 0.034: 1912 0.034 - 0.067: 613 0.067 - 0.101: 219 0.101 - 0.134: 101 0.134 - 0.168: 4 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 7.06e-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: 1.850 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.310 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- 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= 0.117 Angle : 0.554 9.732 24813 Z= 0.304 Chirality : 0.042 0.168 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 0.00236 / 0.12 (18171) covalent geometry : angle 0.54117 / 0.30 (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 : 0.644 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: 0.1453 time to fit residues: 45.2423 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 : 0.464 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113010 restraints weight = 29542.057| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.05 r_work: 0.3276 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0826 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= 0.180 Angle : 0.622 11.046 24813 Z= 0.323 Chirality : 0.045 0.258 2849 Planarity : 0.005 0.041 3058 Dihedral : 11.878 97.853 2912 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.81 % Allowed : 7.27 % Favored : 91.92 % 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: -0.33 (0.18), residues: 2129 helix: 1.48 (0.19), residues: 762 sheet: -0.77 (0.24), residues: 473 loop : -1.38 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 524 TYR 0.017 0.002 TYR C 805 PHE 0.021 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 0.00420 / 0.18 (18171) covalent geometry : angle 0.60796 / 0.32 (24795) hydrogen bonds : bond 0.05582 / 3.76 ( 786) hydrogen bonds : angle 5.30703 / 3.93 ( 2213) metal coordination : bond 0.00568 / 0.39 ( 12) metal coordination : angle 4.97380 / 3.32 ( 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 : 0.450 Fit side-chains revert: symmetry clash REVERT: C 1246 MET cc_start: 0.8155 (mmm) cc_final: 0.7803 (mmm) REVERT: D 83 ASP cc_start: 0.8299 (t0) cc_final: 0.8000 (t0) REVERT: A 55 THR cc_start: 0.8939 (m) cc_final: 0.8661 (m) REVERT: A 393 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7185 (tttt) REVERT: A 815 ARG cc_start: 0.7455 (mmm160) cc_final: 0.6819 (ttt90) REVERT: A 1023 ILE cc_start: 0.7452 (pt) cc_final: 0.7136 (pt) outliers start: 15 outliers final: 9 residues processed: 192 average time/residue: 0.1337 time to fit residues: 38.6322 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 : 0.536 ------------------------------------------------------------------------------- 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 A residue 568 MET 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: 0.8980 chunk 183 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 122 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 666 ASN A 775 ASN A1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.151725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111678 restraints weight = 29695.940| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.84 r_work: 0.3282 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18183 Z= 0.109 Angle : 0.541 7.792 24813 Z= 0.281 Chirality : 0.042 0.345 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.803 101.111 2912 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.08 % Allowed : 9.32 % Favored : 89.60 % 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: 1.51 (0.19), residues: 762 sheet: -0.57 (0.25), residues: 464 loop : -1.30 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 524 TYR 0.017 0.001 TYR C 805 PHE 0.012 0.001 PHE C1126 TRP 0.010 0.001 TRP C 732 HIS 0.003 0.001 HIS A1143 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (18171) covalent geometry : angle 0.53048 / 0.28 (24795) hydrogen bonds : bond 0.04358 / 2.95 ( 786) hydrogen bonds : angle 4.92958 / 3.63 ( 2213) metal coordination : bond 0.00361 / 0.21 ( 12) metal coordination : angle 3.97688 / 2.53 ( 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 209 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7834 (mp0) cc_final: 0.7359 (mp0) REVERT: C 1135 GLU cc_start: 0.8299 (tp30) cc_final: 0.8066 (tp30) REVERT: C 1246 MET cc_start: 0.8078 (mmm) cc_final: 0.7773 (mmm) REVERT: D 12 ARG cc_start: 0.8375 (ptp-110) cc_final: 0.7885 (ptp-110) REVERT: D 83 ASP cc_start: 0.8248 (t0) cc_final: 0.7963 (t0) REVERT: A 55 THR cc_start: 0.8963 (m) cc_final: 0.8677 (m) REVERT: A 393 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6948 (tttt) REVERT: A 706 MET cc_start: 0.3136 (mmm) cc_final: 0.2853 (tpp) REVERT: A 815 ARG cc_start: 0.7402 (mmm160) cc_final: 0.6719 (ttt90) REVERT: A 1023 ILE cc_start: 0.7433 (pt) cc_final: 0.7193 (pt) REVERT: B 72 MET cc_start: 0.8314 (mmm) cc_final: 0.8023 (tpp) outliers start: 20 outliers final: 11 residues processed: 201 average time/residue: 0.1304 time to fit residues: 39.2309 Evaluate side-chains 185 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 971 MET Chi-restraints excluded: chain C residue 1128 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: 1.9990 chunk 182 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 ASN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.149756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110634 restraints weight = 29317.935| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.65 r_work: 0.3249 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1209 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= 0.162 Angle : 0.590 10.208 24813 Z= 0.304 Chirality : 0.045 0.417 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.832 101.757 2912 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.35 % Allowed : 11.15 % Favored : 87.50 % 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: -0.28 (0.18), residues: 2129 helix: 1.47 (0.19), residues: 762 sheet: -0.69 (0.24), residues: 471 loop : -1.35 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1158 TYR 0.019 0.002 TYR C 805 PHE 0.018 0.002 PHE A 788 TRP 0.012 0.002 TRP C 732 HIS 0.008 0.001 HIS C 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (18171) covalent geometry : angle 0.57646 / 0.30 (24795) hydrogen bonds : bond 0.05060 / 3.42 ( 786) hydrogen bonds : angle 4.86296 / 3.56 ( 2213) metal coordination : bond 0.00517 / 0.34 ( 12) metal coordination : angle 4.71492 / 3.09 ( 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 203 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7844 (mp0) cc_final: 0.7309 (mp0) REVERT: C 898 TYR cc_start: 0.7803 (t80) cc_final: 0.7546 (t80) REVERT: C 1033 GLU cc_start: 0.7767 (tp30) cc_final: 0.7554 (tp30) REVERT: C 1056 MET cc_start: 0.7849 (mmm) cc_final: 0.7532 (mmt) REVERT: C 1246 MET cc_start: 0.8123 (mmm) cc_final: 0.7794 (mmm) REVERT: D 12 ARG cc_start: 0.8489 (ptp-110) cc_final: 0.8009 (ptp-110) REVERT: D 83 ASP cc_start: 0.8292 (t0) cc_final: 0.8007 (t0) REVERT: A 55 THR cc_start: 0.9018 (m) cc_final: 0.8708 (m) REVERT: A 393 LYS cc_start: 0.7252 (ttpt) cc_final: 0.6890 (tttt) REVERT: A 815 ARG cc_start: 0.7499 (mmm160) cc_final: 0.6909 (ttt180) REVERT: A 1023 ILE cc_start: 0.7449 (pt) cc_final: 0.7130 (pt) REVERT: A 1191 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7520 (mmtt) REVERT: B 72 MET cc_start: 0.8370 (mmm) cc_final: 0.8103 (tpp) outliers start: 25 outliers final: 18 residues processed: 196 average time/residue: 0.1355 time to fit residues: 39.9840 Evaluate side-chains 189 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 1128 VAL Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain A residue 71 THR 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 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: 7.9990 chunk 215 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 ASN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.151695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111017 restraints weight = 29317.769| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.85 r_work: 0.3278 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1267 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= 0.107 Angle : 0.535 13.471 24813 Z= 0.275 Chirality : 0.043 0.435 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.789 104.188 2912 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.45 % Allowed : 11.85 % Favored : 86.69 % 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: -0.16 (0.18), residues: 2129 helix: 1.54 (0.19), residues: 765 sheet: -0.49 (0.25), residues: 455 loop : -1.33 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1199 TYR 0.020 0.001 TYR C 805 PHE 0.014 0.001 PHE C1126 TRP 0.012 0.001 TRP C 732 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (18171) covalent geometry : angle 0.52461 / 0.27 (24795) hydrogen bonds : bond 0.04091 / 2.78 ( 786) hydrogen bonds : angle 4.65712 / 3.40 ( 2213) metal coordination : bond 0.00385 / 0.23 ( 12) metal coordination : angle 3.92243 / 2.49 ( 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 203 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7739 (mp0) cc_final: 0.7201 (mp0) REVERT: C 1135 GLU cc_start: 0.8358 (tp30) cc_final: 0.8138 (tp30) REVERT: C 1246 MET cc_start: 0.8100 (mmm) cc_final: 0.7799 (mmm) REVERT: D 12 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.7943 (ptp-110) REVERT: D 83 ASP cc_start: 0.8269 (t0) cc_final: 0.7927 (t0) REVERT: A 55 THR cc_start: 0.9001 (m) cc_final: 0.8652 (m) REVERT: A 393 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6897 (tttt) REVERT: A 815 ARG cc_start: 0.7318 (mmm160) cc_final: 0.6772 (ttt90) REVERT: A 1023 ILE cc_start: 0.7425 (pt) cc_final: 0.7096 (pt) REVERT: A 1191 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7530 (mmtt) REVERT: B 14 LEU cc_start: 0.6949 (tp) cc_final: 0.6695 (tp) REVERT: B 72 MET cc_start: 0.8327 (mmm) cc_final: 0.7999 (tpp) outliers start: 27 outliers final: 17 residues processed: 195 average time/residue: 0.1451 time to fit residues: 42.3275 Evaluate side-chains 187 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 1092 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 341 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 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: 2.9990 chunk 201 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 878 ASN A 775 ASN A1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109564 restraints weight = 29047.697| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.76 r_work: 0.3256 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1363 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= 0.140 Angle : 0.559 8.490 24813 Z= 0.288 Chirality : 0.043 0.167 2849 Planarity : 0.004 0.037 3058 Dihedral : 11.792 103.830 2912 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.62 % Allowed : 12.93 % Favored : 85.45 % 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: -0.22 (0.18), residues: 2129 helix: 1.51 (0.19), residues: 765 sheet: -0.56 (0.24), residues: 456 loop : -1.37 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1057 TYR 0.020 0.001 TYR C 805 PHE 0.016 0.001 PHE A 788 TRP 0.012 0.001 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18171) covalent geometry : angle 0.54748 / 0.29 (24795) hydrogen bonds : bond 0.04590 / 3.11 ( 786) hydrogen bonds : angle 4.65411 / 3.40 ( 2213) metal coordination : bond 0.00466 / 0.31 ( 12) metal coordination : angle 4.26562 / 2.76 ( 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 202 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: C 898 TYR cc_start: 0.7852 (t80) cc_final: 0.7594 (t80) REVERT: C 1246 MET cc_start: 0.8072 (mmm) cc_final: 0.7721 (mmm) REVERT: D 12 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.7871 (ptp-110) REVERT: D 83 ASP cc_start: 0.8294 (t0) cc_final: 0.7954 (t0) REVERT: A 55 THR cc_start: 0.8987 (m) cc_final: 0.8706 (m) REVERT: A 393 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6842 (tttt) REVERT: A 583 MET cc_start: 0.3304 (tpp) cc_final: 0.2390 (mmm) REVERT: A 706 MET cc_start: 0.3853 (mpp) cc_final: 0.2713 (ttt) REVERT: A 815 ARG cc_start: 0.7439 (mmm160) cc_final: 0.6733 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7388 (pt) cc_final: 0.7076 (pt) REVERT: A 1191 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7474 (mmtt) REVERT: B 14 LEU cc_start: 0.6724 (tp) cc_final: 0.6447 (tp) REVERT: B 72 MET cc_start: 0.8356 (mmm) cc_final: 0.8050 (tpp) outliers start: 30 outliers final: 23 residues processed: 193 average time/residue: 0.1413 time to fit residues: 41.0602 Evaluate side-chains 192 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 777 PHE Chi-restraints excluded: chain C residue 971 MET 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 1281 ILE 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 533 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: 2.9990 chunk 163 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 ASN A 941 HIS A1017 ASN B 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109158 restraints weight = 29455.198| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.78 r_work: 0.3244 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1469 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= 0.147 Angle : 0.571 9.053 24813 Z= 0.295 Chirality : 0.044 0.268 2849 Planarity : 0.004 0.037 3058 Dihedral : 11.811 104.567 2912 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.83 % Allowed : 12.93 % Favored : 85.24 % 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: 1.47 (0.19), residues: 771 sheet: -0.55 (0.24), residues: 457 loop : -1.44 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1199 TYR 0.014 0.001 TYR A 189 PHE 0.017 0.001 PHE A 234 TRP 0.015 0.001 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (18171) covalent geometry : angle 0.55853 / 0.29 (24795) hydrogen bonds : bond 0.04726 / 3.19 ( 786) hydrogen bonds : angle 4.66535 / 3.40 ( 2213) metal coordination : bond 0.00515 / 0.35 ( 12) metal coordination : angle 4.50492 / 2.96 ( 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 209 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: C 805 TYR cc_start: 0.7953 (t80) cc_final: 0.7287 (t80) REVERT: C 809 GLU cc_start: 0.7835 (mp0) cc_final: 0.7276 (mp0) REVERT: C 898 TYR cc_start: 0.7865 (t80) cc_final: 0.7500 (t80) REVERT: C 1135 GLU cc_start: 0.8340 (tp30) cc_final: 0.8130 (tp30) REVERT: D 83 ASP cc_start: 0.8298 (t0) cc_final: 0.7901 (t0) REVERT: A 55 THR cc_start: 0.9000 (m) cc_final: 0.8721 (m) REVERT: A 393 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6748 (tttt) REVERT: A 583 MET cc_start: 0.3228 (tpp) cc_final: 0.2549 (mmm) REVERT: A 706 MET cc_start: 0.3965 (mpp) cc_final: 0.2707 (ttt) REVERT: A 815 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6861 (tpt-90) REVERT: A 1023 ILE cc_start: 0.7383 (pt) cc_final: 0.7079 (pt) REVERT: A 1191 LYS cc_start: 0.7884 (mttt) cc_final: 0.7480 (mmtt) REVERT: B 14 LEU cc_start: 0.6893 (tp) cc_final: 0.6634 (tp) REVERT: B 72 MET cc_start: 0.8384 (mmm) cc_final: 0.8092 (tpp) outliers start: 34 outliers final: 23 residues processed: 198 average time/residue: 0.1371 time to fit residues: 40.9363 Evaluate side-chains 194 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 1092 ASP 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 197 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 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: 6.9990 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 168 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 94 optimal weight: 0.2980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 878 ASN C 886 HIS A1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.152179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111717 restraints weight = 29208.310| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.77 r_work: 0.3278 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18183 Z= 0.101 Angle : 0.525 7.645 24813 Z= 0.272 Chirality : 0.042 0.174 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.720 106.076 2912 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.24 % Allowed : 13.95 % 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: -0.10 (0.18), residues: 2129 helix: 1.60 (0.19), residues: 770 sheet: -0.37 (0.25), residues: 444 loop : -1.37 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1199 TYR 0.017 0.001 TYR C 979 PHE 0.015 0.001 PHE C1126 TRP 0.011 0.001 TRP C 732 HIS 0.003 0.001 HIS C 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (18171) covalent geometry : angle 0.51685 / 0.27 (24795) hydrogen bonds : bond 0.03686 / 2.51 ( 786) hydrogen bonds : angle 4.46828 / 3.26 ( 2213) metal coordination : bond 0.00339 / 0.20 ( 12) metal coordination : angle 3.52958 / 2.14 ( 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 204 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1135 GLU cc_start: 0.8334 (tp30) cc_final: 0.8124 (tp30) REVERT: D 83 ASP cc_start: 0.8275 (t0) cc_final: 0.7886 (t0) REVERT: A 55 THR cc_start: 0.8920 (m) cc_final: 0.8642 (p) REVERT: A 393 LYS cc_start: 0.7214 (ttpt) cc_final: 0.6798 (tttt) REVERT: A 706 MET cc_start: 0.3977 (mpp) cc_final: 0.2747 (ttt) REVERT: A 815 ARG cc_start: 0.7445 (mmm160) cc_final: 0.6850 (ttt90) REVERT: A 1023 ILE cc_start: 0.7310 (pt) cc_final: 0.7006 (pt) REVERT: A 1191 LYS cc_start: 0.7875 (mttt) cc_final: 0.7496 (mmtt) REVERT: B 14 LEU cc_start: 0.6707 (tp) cc_final: 0.6496 (tp) outliers start: 23 outliers final: 17 residues processed: 197 average time/residue: 0.1281 time to fit residues: 38.2734 Evaluate side-chains 188 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 197 THR Chi-restraints excluded: chain A residue 533 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 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: 3.9990 chunk 4 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.151714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111167 restraints weight = 29348.851| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.82 r_work: 0.3267 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1537 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= 0.105 Angle : 0.529 8.319 24813 Z= 0.274 Chirality : 0.042 0.173 2849 Planarity : 0.004 0.037 3058 Dihedral : 11.677 105.370 2912 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.19 % Allowed : 14.66 % Favored : 84.16 % 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: -0.06 (0.18), residues: 2129 helix: 1.64 (0.19), residues: 772 sheet: -0.35 (0.25), residues: 443 loop : -1.36 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 775 TYR 0.018 0.001 TYR C 805 PHE 0.013 0.001 PHE C1126 TRP 0.015 0.001 TRP C 732 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (18171) covalent geometry : angle 0.52023 / 0.27 (24795) hydrogen bonds : bond 0.03822 / 2.60 ( 786) hydrogen bonds : angle 4.43168 / 3.24 ( 2213) metal coordination : bond 0.00335 / 0.20 ( 12) metal coordination : angle 3.57508 / 2.22 ( 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 198 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 83 ASP cc_start: 0.8273 (t0) cc_final: 0.7874 (t0) REVERT: A 55 THR cc_start: 0.8945 (m) cc_final: 0.8659 (p) REVERT: A 393 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6806 (tttt) REVERT: A 583 MET cc_start: 0.3284 (tpp) cc_final: 0.2752 (mmp) REVERT: A 706 MET cc_start: 0.4000 (mpp) cc_final: 0.2918 (ttt) REVERT: A 815 ARG cc_start: 0.7475 (mmm160) cc_final: 0.6836 (ttt90) REVERT: A 1023 ILE cc_start: 0.7345 (pt) cc_final: 0.7047 (pt) REVERT: A 1191 LYS cc_start: 0.7866 (mttt) cc_final: 0.7513 (mmtt) REVERT: B 14 LEU cc_start: 0.6810 (tp) cc_final: 0.6500 (tp) outliers start: 22 outliers final: 19 residues processed: 192 average time/residue: 0.1232 time to fit residues: 36.5746 Evaluate side-chains 190 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 835 ASP 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 197 THR Chi-restraints excluded: chain A residue 533 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 143 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.151743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111138 restraints weight = 29260.915| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.78 r_work: 0.3279 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1580 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= 0.105 Angle : 0.530 8.517 24813 Z= 0.274 Chirality : 0.042 0.170 2849 Planarity : 0.004 0.037 3058 Dihedral : 11.654 105.614 2912 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.24 % Allowed : 14.60 % Favored : 84.16 % 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: -0.03 (0.18), residues: 2129 helix: 1.64 (0.19), residues: 772 sheet: -0.29 (0.25), residues: 459 loop : -1.36 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 775 TYR 0.017 0.001 TYR C 979 PHE 0.013 0.001 PHE C1126 TRP 0.019 0.001 TRP C 732 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (18171) covalent geometry : angle 0.52135 / 0.27 (24795) hydrogen bonds : bond 0.03800 / 2.59 ( 786) hydrogen bonds : angle 4.41088 / 3.22 ( 2213) metal coordination : bond 0.00332 / 0.21 ( 12) metal coordination : angle 3.51121 / 2.18 ( 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 199 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 949 GLN cc_start: 0.7268 (pt0) cc_final: 0.7005 (pt0) REVERT: C 1135 GLU cc_start: 0.8287 (tp30) cc_final: 0.8006 (tp30) REVERT: D 83 ASP cc_start: 0.8307 (t0) cc_final: 0.7921 (t0) REVERT: A 55 THR cc_start: 0.8958 (m) cc_final: 0.8657 (p) REVERT: A 393 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6813 (tttt) REVERT: A 583 MET cc_start: 0.3177 (tpp) cc_final: 0.2662 (mmp) REVERT: A 706 MET cc_start: 0.4073 (mpp) cc_final: 0.2852 (ttt) REVERT: A 815 ARG cc_start: 0.7533 (mmm160) cc_final: 0.6877 (ttt90) REVERT: A 1023 ILE cc_start: 0.7340 (pt) cc_final: 0.7042 (pt) REVERT: A 1191 LYS cc_start: 0.7862 (mttt) cc_final: 0.7508 (mmtt) REVERT: B 13 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.5568 (t-90) REVERT: B 14 LEU cc_start: 0.6751 (tp) cc_final: 0.6455 (tp) outliers start: 23 outliers final: 21 residues processed: 192 average time/residue: 0.1325 time to fit residues: 38.7494 Evaluate side-chains 196 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 835 ASP Chi-restraints excluded: chain C residue 971 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 197 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 13 HIS 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: 2.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 121 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110558 restraints weight = 29500.658| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.87 r_work: 0.3253 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18183 Z= 0.113 Angle : 0.538 8.456 24813 Z= 0.278 Chirality : 0.042 0.169 2849 Planarity : 0.004 0.037 3058 Dihedral : 11.641 105.394 2912 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.29 % Allowed : 14.66 % Favored : 84.05 % 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: -0.05 (0.18), residues: 2129 helix: 1.64 (0.19), residues: 772 sheet: -0.27 (0.24), residues: 466 loop : -1.41 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 524 TYR 0.016 0.001 TYR C 979 PHE 0.014 0.001 PHE A 788 TRP 0.025 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18171) covalent geometry : angle 0.52860 / 0.28 (24795) hydrogen bonds : bond 0.03974 / 2.70 ( 786) hydrogen bonds : angle 4.42277 / 3.23 ( 2213) metal coordination : bond 0.00371 / 0.24 ( 12) metal coordination : angle 3.74392 / 2.37 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.82 seconds wall clock time: 87 minutes 24.32 seconds (5244.32 seconds total)