Starting phenix.real_space_refine on Thu Feb 5 14:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1y_61984/02_2026/9k1y_61984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1y_61984/02_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_61984/02_2026/9k1y_61984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1y_61984/02_2026/9k1y_61984.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1y_61984/02_2026/9k1y_61984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1y_61984/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17743 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6421 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 34, 'TRANS': 773} Chain: "D" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "A" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9139 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 60, 'TRANS': 1104} Chain breaks: 5 Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 584 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 505 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 19} Chain: "H" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6590 SG CYS D 23 86.098 61.846 42.655 1.00 34.70 S ATOM 6614 SG CYS D 26 83.854 58.947 43.343 1.00 35.58 S ATOM 6861 SG CYS D 58 85.384 61.051 46.210 1.00 32.20 S ATOM 6882 SG CYS D 61 87.649 58.759 44.153 1.00 34.61 S ATOM 6503 SG CYS D 11 86.818 55.494 60.374 1.00 29.44 S ATOM 6766 SG CYS D 46 86.482 59.170 61.799 1.00 31.21 S ATOM 6789 SG CYS D 49 87.574 58.682 58.376 1.00 36.31 S ATOM 7060 SG CYS D 85 83.921 57.489 59.576 1.00 26.39 S ATOM 6641 SG CYS D 30 73.070 57.438 49.178 1.00 28.76 S ATOM 6662 SG CYS D 33 71.849 54.251 47.591 1.00 29.77 S ATOM 6957 SG CYS D 72 69.301 56.802 48.657 1.00 26.68 S ATOM 6981 SG CYS D 75 71.058 54.908 51.308 1.00 22.69 S Time building chain proxies: 3.11, per 1000 atoms: 0.18 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: 0.95 Conformation dependent library (CDL) restraints added in 708.5 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: 1.97 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: 2.91 Time building geometry restraints manager: 1.31 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=" 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 bond pdb=" CG GLU C 595 " pdb=" CD GLU C 595 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.52e-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=" 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 angle pdb=" CA SER A 717 " pdb=" C SER A 717 " pdb=" N ARG A 718 " ideal model delta sigma weight residual 119.26 115.70 3.56 1.14e+00 7.69e-01 9.73e+00 ... (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: 1.360 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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= 0.113 Angle : 0.554 9.732 24813 Z= 0.287 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 covalent geometry : bond 0.00236 (18171) covalent geometry : angle 0.54115 (24795) hydrogen bonds : bond 0.17157 ( 786) hydrogen bonds : angle 6.67889 ( 2213) metal coordination : bond 0.00405 ( 12) metal coordination : angle 4.39916 ( 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 : 0.653 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: 0.1377 time to fit residues: 42.8658 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 : 0.504 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 949 GLN C1142 ASN A 666 ASN A1017 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112174 restraints weight = 29536.264| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.97 r_work: 0.3270 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1067 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= 0.179 Angle : 0.637 12.025 24813 Z= 0.326 Chirality : 0.045 0.195 2849 Planarity : 0.005 0.046 3058 Dihedral : 11.898 98.645 2912 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.86 % Allowed : 7.70 % Favored : 91.43 % 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: -0.37 (0.18), residues: 2129 helix: 1.42 (0.19), residues: 765 sheet: -0.88 (0.24), residues: 474 loop : -1.34 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 524 TYR 0.016 0.002 TYR A 189 PHE 0.021 0.002 PHE A 234 TRP 0.012 0.002 TRP C 732 HIS 0.008 0.001 HIS A1143 Details of bonding type rmsd covalent geometry : bond 0.00421 (18171) covalent geometry : angle 0.62005 (24795) hydrogen bonds : bond 0.05573 ( 786) hydrogen bonds : angle 5.15015 ( 2213) metal coordination : bond 0.00658 ( 12) metal coordination : angle 5.48803 ( 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 199 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: C 1037 ASP cc_start: 0.8017 (m-30) cc_final: 0.7744 (m-30) REVERT: C 1056 MET cc_start: 0.7769 (mmm) cc_final: 0.7479 (mmt) REVERT: C 1246 MET cc_start: 0.8064 (mmm) cc_final: 0.7703 (mmm) REVERT: D 83 ASP cc_start: 0.8335 (t0) cc_final: 0.8117 (t0) REVERT: A 55 THR cc_start: 0.8910 (m) cc_final: 0.8636 (m) REVERT: A 393 LYS cc_start: 0.7263 (ttpt) cc_final: 0.6946 (tttt) REVERT: A 815 ARG cc_start: 0.7629 (mmm160) cc_final: 0.6962 (ttt90) REVERT: A 1023 ILE cc_start: 0.7429 (pt) cc_final: 0.7113 (pt) outliers start: 16 outliers final: 10 residues processed: 192 average time/residue: 0.1444 time to fit residues: 41.6960 Evaluate side-chains 178 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 71 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109933 restraints weight = 29687.377| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.78 r_work: 0.3245 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1183 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= 0.126 Angle : 0.569 8.727 24813 Z= 0.291 Chirality : 0.043 0.331 2849 Planarity : 0.004 0.040 3058 Dihedral : 11.847 102.956 2912 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.08 % Allowed : 10.67 % Favored : 88.25 % 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: -0.29 (0.18), residues: 2129 helix: 1.47 (0.19), residues: 762 sheet: -0.71 (0.24), residues: 470 loop : -1.35 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1057 TYR 0.022 0.001 TYR C 830 PHE 0.014 0.001 PHE A 234 TRP 0.010 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00283 (18171) covalent geometry : angle 0.55585 (24795) hydrogen bonds : bond 0.04587 ( 786) hydrogen bonds : angle 4.83928 ( 2213) metal coordination : bond 0.00459 ( 12) metal coordination : angle 4.56098 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7864 (mp0) cc_final: 0.7323 (mp0) REVERT: C 1033 GLU cc_start: 0.7920 (tp30) cc_final: 0.7597 (tp30) REVERT: C 1037 ASP cc_start: 0.8035 (m-30) cc_final: 0.7673 (m-30) REVERT: C 1056 MET cc_start: 0.7912 (mmm) cc_final: 0.7579 (mmt) REVERT: C 1135 GLU cc_start: 0.8362 (tp30) cc_final: 0.8158 (tp30) REVERT: C 1246 MET cc_start: 0.8058 (mmm) cc_final: 0.7721 (mmm) REVERT: D 83 ASP cc_start: 0.8288 (t0) cc_final: 0.7933 (t0) REVERT: A 55 THR cc_start: 0.8993 (m) cc_final: 0.8706 (m) REVERT: A 393 LYS cc_start: 0.7257 (ttpt) cc_final: 0.6907 (tttt) REVERT: A 706 MET cc_start: 0.3994 (mpp) cc_final: 0.2814 (ttt) REVERT: A 815 ARG cc_start: 0.7600 (mmm160) cc_final: 0.6894 (ttt90) REVERT: A 1023 ILE cc_start: 0.7433 (pt) cc_final: 0.7103 (pt) REVERT: B 72 MET cc_start: 0.8343 (mmm) cc_final: 0.8038 (tpp) outliers start: 20 outliers final: 13 residues processed: 197 average time/residue: 0.1425 time to fit residues: 41.7539 Evaluate side-chains 184 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 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: 0.9980 chunk 98 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.150831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110265 restraints weight = 29300.633| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.94 r_work: 0.3256 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1350 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= 0.120 Angle : 0.548 8.196 24813 Z= 0.280 Chirality : 0.042 0.171 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.811 104.335 2912 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.56 % Allowed : 11.64 % Favored : 86.80 % 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: -0.24 (0.18), residues: 2129 helix: 1.50 (0.19), residues: 765 sheet: -0.55 (0.25), residues: 449 loop : -1.39 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1057 TYR 0.019 0.001 TYR C 805 PHE 0.013 0.001 PHE A 234 TRP 0.012 0.001 TRP C 732 HIS 0.004 0.001 HIS C 572 Details of bonding type rmsd covalent geometry : bond 0.00270 (18171) covalent geometry : angle 0.53593 (24795) hydrogen bonds : bond 0.04311 ( 786) hydrogen bonds : angle 4.66128 ( 2213) metal coordination : bond 0.00432 ( 12) metal coordination : angle 4.23434 ( 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: 29 poor density : 174 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: C 898 TYR cc_start: 0.7916 (t80) cc_final: 0.7673 (t80) REVERT: C 1033 GLU cc_start: 0.7909 (tp30) cc_final: 0.7398 (tp30) REVERT: C 1037 ASP cc_start: 0.8130 (m-30) cc_final: 0.7314 (m-30) REVERT: C 1246 MET cc_start: 0.8035 (mmm) cc_final: 0.7732 (mmm) REVERT: D 83 ASP cc_start: 0.8287 (t0) cc_final: 0.7913 (t0) REVERT: A 55 THR cc_start: 0.8990 (m) cc_final: 0.8691 (m) REVERT: A 393 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6866 (tttt) REVERT: A 706 MET cc_start: 0.3973 (mpp) cc_final: 0.3005 (ttt) REVERT: A 712 VAL cc_start: 0.2558 (OUTLIER) cc_final: 0.2353 (p) REVERT: A 815 ARG cc_start: 0.7578 (mmm160) cc_final: 0.6900 (ttt90) REVERT: A 1023 ILE cc_start: 0.7363 (pt) cc_final: 0.7050 (pt) REVERT: A 1191 LYS cc_start: 0.7971 (mttt) cc_final: 0.7501 (mmtt) REVERT: B 72 MET cc_start: 0.8337 (mmm) cc_final: 0.8028 (tpp) outliers start: 29 outliers final: 24 residues processed: 196 average time/residue: 0.1396 time to fit residues: 41.1580 Evaluate side-chains 190 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1092 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 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 30 GLU 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: 6.9990 chunk 215 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 941 HIS A1017 ASN B 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.149497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109386 restraints weight = 29439.455| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.62 r_work: 0.3249 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1527 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= 0.150 Angle : 0.582 9.302 24813 Z= 0.297 Chirality : 0.044 0.207 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.836 104.761 2912 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.05 % Allowed : 12.23 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2129 helix: 1.42 (0.19), residues: 768 sheet: -0.58 (0.25), residues: 449 loop : -1.43 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1238 TYR 0.020 0.001 TYR C 805 PHE 0.018 0.001 PHE A 234 TRP 0.013 0.002 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00349 (18171) covalent geometry : angle 0.56801 (24795) hydrogen bonds : bond 0.04832 ( 786) hydrogen bonds : angle 4.69067 ( 2213) metal coordination : bond 0.00514 ( 12) metal coordination : angle 4.77437 ( 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 213 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7864 (mp0) cc_final: 0.7335 (mp0) REVERT: C 879 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8292 (mm) REVERT: C 1033 GLU cc_start: 0.7765 (tp30) cc_final: 0.7144 (tp30) REVERT: C 1037 ASP cc_start: 0.7979 (m-30) cc_final: 0.7010 (m-30) REVERT: C 1135 GLU cc_start: 0.8443 (tp30) cc_final: 0.8236 (tp30) REVERT: D 83 ASP cc_start: 0.8280 (t0) cc_final: 0.7895 (t0) REVERT: A 55 THR cc_start: 0.9012 (m) cc_final: 0.8692 (m) REVERT: A 393 LYS cc_start: 0.7252 (ttpt) cc_final: 0.7010 (tttt) REVERT: A 706 MET cc_start: 0.4083 (mpp) cc_final: 0.3153 (ttt) REVERT: A 815 ARG cc_start: 0.7547 (mmm160) cc_final: 0.6895 (ttt90) REVERT: A 1023 ILE cc_start: 0.7419 (pt) cc_final: 0.7113 (pt) REVERT: A 1191 LYS cc_start: 0.7910 (mttt) cc_final: 0.7456 (mmtt) REVERT: B 72 MET cc_start: 0.8378 (mmm) cc_final: 0.8093 (tpp) outliers start: 38 outliers final: 27 residues processed: 201 average time/residue: 0.1452 time to fit residues: 43.8199 Evaluate side-chains 195 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 879 LEU Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 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 30 GLU Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 0.0870 chunk 166 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN B 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.148951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108792 restraints weight = 29409.817| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.00 r_work: 0.3226 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18183 Z= 0.151 Angle : 0.581 9.120 24813 Z= 0.297 Chirality : 0.043 0.184 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.831 104.986 2912 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.37 % Allowed : 13.15 % Favored : 84.48 % 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: -0.32 (0.18), residues: 2129 helix: 1.43 (0.19), residues: 769 sheet: -0.61 (0.24), residues: 458 loop : -1.45 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1158 TYR 0.019 0.001 TYR C 805 PHE 0.017 0.001 PHE A 234 TRP 0.013 0.002 TRP C 732 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00352 (18171) covalent geometry : angle 0.56772 (24795) hydrogen bonds : bond 0.04796 ( 786) hydrogen bonds : angle 4.65575 ( 2213) metal coordination : bond 0.00539 ( 12) metal coordination : angle 4.70145 ( 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 214 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: C 879 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8254 (mm) REVERT: C 898 TYR cc_start: 0.7828 (t80) cc_final: 0.7610 (t80) REVERT: C 1135 GLU cc_start: 0.8359 (tp30) cc_final: 0.8152 (tp30) REVERT: D 83 ASP cc_start: 0.8288 (t0) cc_final: 0.8064 (t0) REVERT: A 55 THR cc_start: 0.9033 (m) cc_final: 0.8709 (m) REVERT: A 393 LYS cc_start: 0.7414 (ttpt) cc_final: 0.7175 (tttt) REVERT: A 583 MET cc_start: 0.3471 (tpp) cc_final: 0.2600 (mmm) REVERT: A 815 ARG cc_start: 0.7531 (mmm160) cc_final: 0.6864 (ttt90) REVERT: A 1023 ILE cc_start: 0.7414 (pt) cc_final: 0.7111 (pt) REVERT: A 1191 LYS cc_start: 0.7901 (mttt) cc_final: 0.7454 (mmtt) REVERT: B 72 MET cc_start: 0.8379 (mmm) cc_final: 0.8079 (tpp) outliers start: 44 outliers final: 31 residues processed: 200 average time/residue: 0.1416 time to fit residues: 43.1484 Evaluate side-chains 199 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 675 MET Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 879 LEU 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 1206 ASP Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 30 GLU 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: 8.9990 chunk 210 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN B 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.149315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109337 restraints weight = 29739.532| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.07 r_work: 0.3232 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18183 Z= 0.133 Angle : 0.573 9.267 24813 Z= 0.291 Chirality : 0.043 0.173 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.813 105.168 2912 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.16 % Allowed : 14.39 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2129 helix: 1.50 (0.19), residues: 773 sheet: -0.56 (0.24), residues: 457 loop : -1.43 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1057 TYR 0.021 0.001 TYR C 805 PHE 0.015 0.001 PHE A 234 TRP 0.012 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00306 (18171) covalent geometry : angle 0.55812 (24795) hydrogen bonds : bond 0.04525 ( 786) hydrogen bonds : angle 4.59645 ( 2213) metal coordination : bond 0.00491 ( 12) metal coordination : angle 4.84755 ( 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 215 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: C 809 GLU cc_start: 0.7833 (mp0) cc_final: 0.7282 (mp0) REVERT: C 1135 GLU cc_start: 0.8396 (tp30) cc_final: 0.8179 (tp30) REVERT: D 83 ASP cc_start: 0.8323 (t0) cc_final: 0.8077 (t0) REVERT: A 55 THR cc_start: 0.9022 (m) cc_final: 0.8696 (m) REVERT: A 393 LYS cc_start: 0.7374 (ttpt) cc_final: 0.7153 (tttt) REVERT: A 706 MET cc_start: 0.4058 (mpp) cc_final: 0.2832 (ttt) REVERT: A 815 ARG cc_start: 0.7584 (mmm160) cc_final: 0.6904 (ttt90) REVERT: A 1023 ILE cc_start: 0.7437 (pt) cc_final: 0.7137 (pt) REVERT: A 1191 LYS cc_start: 0.7878 (mttt) cc_final: 0.7447 (mmtt) REVERT: B 72 MET cc_start: 0.8338 (mmm) cc_final: 0.8035 (tpp) outliers start: 40 outliers final: 32 residues processed: 202 average time/residue: 0.1396 time to fit residues: 42.3294 Evaluate side-chains 203 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 675 MET 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 1092 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 30 GLU 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: 0.9980 chunk 83 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN B 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109488 restraints weight = 29559.527| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.63 r_work: 0.3252 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1685 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= 0.120 Angle : 0.567 10.909 24813 Z= 0.286 Chirality : 0.043 0.368 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.781 105.091 2912 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.89 % Allowed : 14.55 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2129 helix: 1.53 (0.19), residues: 773 sheet: -0.49 (0.24), residues: 449 loop : -1.42 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1199 TYR 0.022 0.001 TYR C 805 PHE 0.014 0.001 PHE C1126 TRP 0.012 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00271 (18171) covalent geometry : angle 0.55418 (24795) hydrogen bonds : bond 0.04225 ( 786) hydrogen bonds : angle 4.52808 ( 2213) metal coordination : bond 0.00435 ( 12) metal coordination : angle 4.43618 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: C 805 TYR cc_start: 0.7620 (t80) cc_final: 0.7360 (t80) REVERT: C 809 GLU cc_start: 0.7827 (mp0) cc_final: 0.7279 (mp0) REVERT: C 876 MET cc_start: 0.8321 (mmt) cc_final: 0.8107 (mmm) REVERT: C 1135 GLU cc_start: 0.8335 (tp30) cc_final: 0.8118 (tp30) REVERT: D 83 ASP cc_start: 0.8283 (t0) cc_final: 0.7876 (t0) REVERT: A 55 THR cc_start: 0.8988 (m) cc_final: 0.8567 (m) REVERT: A 393 LYS cc_start: 0.7369 (ttpt) cc_final: 0.7155 (tttt) REVERT: A 706 MET cc_start: 0.3855 (mpp) cc_final: 0.2848 (ttt) REVERT: A 815 ARG cc_start: 0.7609 (mmm160) cc_final: 0.6945 (ttt90) REVERT: A 1023 ILE cc_start: 0.7420 (pt) cc_final: 0.7118 (pt) REVERT: A 1191 LYS cc_start: 0.7893 (mttt) cc_final: 0.7457 (mmtt) REVERT: B 72 MET cc_start: 0.8314 (mmm) cc_final: 0.7988 (tpp) outliers start: 35 outliers final: 25 residues processed: 203 average time/residue: 0.1332 time to fit residues: 40.9190 Evaluate side-chains 196 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 1128 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 425 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 30 GLU Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 153 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.150883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110614 restraints weight = 29603.292| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.52 r_work: 0.3270 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18183 Z= 0.107 Angle : 0.548 8.666 24813 Z= 0.278 Chirality : 0.042 0.270 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.719 105.089 2912 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.56 % Allowed : 15.30 % Favored : 83.14 % 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: -0.11 (0.18), residues: 2129 helix: 1.59 (0.19), residues: 772 sheet: -0.31 (0.25), residues: 451 loop : -1.43 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1057 TYR 0.022 0.001 TYR C 805 PHE 0.014 0.001 PHE C1126 TRP 0.011 0.001 TRP C 732 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00234 (18171) covalent geometry : angle 0.53763 (24795) hydrogen bonds : bond 0.03864 ( 786) hydrogen bonds : angle 4.43398 ( 2213) metal coordination : bond 0.00369 ( 12) metal coordination : angle 4.00454 ( 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 201 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 876 MET cc_start: 0.8276 (mmt) cc_final: 0.8076 (mmm) REVERT: C 1135 GLU cc_start: 0.8291 (tp30) cc_final: 0.8042 (tp30) REVERT: D 83 ASP cc_start: 0.8240 (t0) cc_final: 0.7901 (t0) REVERT: A 55 THR cc_start: 0.8925 (m) cc_final: 0.8585 (p) REVERT: A 393 LYS cc_start: 0.7226 (ttpt) cc_final: 0.6993 (tttt) REVERT: A 447 MET cc_start: 0.1779 (mtp) cc_final: 0.1549 (mtp) REVERT: A 706 MET cc_start: 0.3869 (mpp) cc_final: 0.2786 (ttt) REVERT: A 815 ARG cc_start: 0.7554 (mmm160) cc_final: 0.6944 (ttt90) REVERT: A 1191 LYS cc_start: 0.7869 (mttt) cc_final: 0.7471 (mmtt) REVERT: B 13 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.5626 (t-90) outliers start: 29 outliers final: 25 residues processed: 193 average time/residue: 0.1525 time to fit residues: 43.9716 Evaluate side-chains 192 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 30 GLU 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: 0.9990 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 153 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.150012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109130 restraints weight = 29319.897| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.95 r_work: 0.3258 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18183 Z= 0.128 Angle : 0.574 9.222 24813 Z= 0.289 Chirality : 0.043 0.267 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.730 104.520 2912 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.62 % Allowed : 15.57 % Favored : 82.81 % 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: -0.17 (0.18), residues: 2129 helix: 1.57 (0.19), residues: 766 sheet: -0.37 (0.24), residues: 459 loop : -1.46 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 524 TYR 0.015 0.001 TYR C 979 PHE 0.015 0.001 PHE A 234 TRP 0.016 0.001 TRP C 732 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00294 (18171) covalent geometry : angle 0.56112 (24795) hydrogen bonds : bond 0.04343 ( 786) hydrogen bonds : angle 4.48595 ( 2213) metal coordination : bond 0.00445 ( 12) metal coordination : angle 4.47564 ( 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 198 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 876 MET cc_start: 0.8264 (mmt) cc_final: 0.8037 (mmm) REVERT: C 1135 GLU cc_start: 0.8375 (tp30) cc_final: 0.8132 (tp30) REVERT: D 83 ASP cc_start: 0.8320 (t0) cc_final: 0.7954 (t0) REVERT: A 55 THR cc_start: 0.8953 (m) cc_final: 0.8613 (p) REVERT: A 304 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8039 (tp-100) REVERT: A 393 LYS cc_start: 0.7376 (ttpt) cc_final: 0.6952 (tttt) REVERT: A 447 MET cc_start: 0.1869 (mtp) cc_final: 0.1588 (mtp) REVERT: A 706 MET cc_start: 0.3505 (mpp) cc_final: 0.2403 (ttt) REVERT: A 815 ARG cc_start: 0.7500 (mmm160) cc_final: 0.6837 (ttt90) REVERT: A 1191 LYS cc_start: 0.7892 (mttt) cc_final: 0.7431 (mmtt) REVERT: B 13 HIS cc_start: 0.6411 (OUTLIER) cc_final: 0.5559 (t-90) outliers start: 30 outliers final: 27 residues processed: 190 average time/residue: 0.1321 time to fit residues: 38.1952 Evaluate side-chains 196 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 777 PHE Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 30 GLU 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: 4.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 18 optimal weight: 0.0020 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 737 GLN A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111116 restraints weight = 29636.274| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.83 r_work: 0.3278 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1822 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= 0.105 Angle : 0.543 8.623 24813 Z= 0.275 Chirality : 0.042 0.259 2849 Planarity : 0.004 0.038 3058 Dihedral : 11.679 105.136 2912 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.62 % Allowed : 15.46 % Favored : 82.92 % 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: -0.07 (0.18), residues: 2129 helix: 1.64 (0.19), residues: 767 sheet: -0.24 (0.24), residues: 459 loop : -1.44 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 524 TYR 0.020 0.001 TYR C 805 PHE 0.013 0.001 PHE C1126 TRP 0.017 0.001 TRP C 732 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00230 (18171) covalent geometry : angle 0.53309 (24795) hydrogen bonds : bond 0.03738 ( 786) hydrogen bonds : angle 4.37238 ( 2213) metal coordination : bond 0.00352 ( 12) metal coordination : angle 3.86354 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5255.30 seconds wall clock time: 90 minutes 20.31 seconds (5420.31 seconds total)