Starting phenix.real_space_refine on Tue Mar 12 13:19:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/03_2024/8dy9_27778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/03_2024/8dy9_27778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/03_2024/8dy9_27778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/03_2024/8dy9_27778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/03_2024/8dy9_27778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy9_27778/03_2024/8dy9_27778_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 1.038 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: 9 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 P 143 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 19778 2.51 5 N 5779 2.21 5 O 6473 1.98 5 H 31140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 62": "OE1" <-> "OE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "C ASP 788": "OD1" <-> "OD2" Residue "C GLU 834": "OE1" <-> "OE2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 63435 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3519 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Chain: "B" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4908 Classifications: {'peptide': 319} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Chain: "C" Number of atoms: 17368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 17368 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1060} Chain: "D" Number of atoms: 19789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 19789 Classifications: {'peptide': 1253} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1199} Chain breaks: 1 Chain: "E" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1202 Classifications: {'peptide': 77} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4873 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "G" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1657 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "H" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1158 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4496 Classifications: {'peptide': 303} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 291} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "O" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1197 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "P" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1209 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "Q" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1096 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "R" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 951 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39972 SG CYS D 886 17.847 115.009 90.208 1.00 63.78 S ATOM 41111 SG CYS D 962 21.461 114.786 91.466 1.00 62.70 S ATOM 41194 SG CYS D 969 20.288 113.014 88.150 1.00 57.34 S ATOM 41234 SG CYS D 972 20.757 116.591 88.248 1.00 56.95 S ATOM 26743 SG CYS D 60 53.484 64.128 118.695 1.00 87.50 S ATOM 26774 SG CYS D 62 55.402 63.067 121.730 1.00 89.25 S ATOM 27007 SG CYS D 75 51.645 63.071 121.890 1.00 98.05 S ATOM 27056 SG CYS D 78 53.471 66.335 121.941 1.00 91.51 S ATOM 53526 SG CYS H 25 57.965 45.973 75.138 1.00 56.96 S ATOM 53866 SG CYS H 48 59.855 40.076 73.728 1.00 67.31 S ATOM 53996 SG CYS H 57 63.574 43.661 77.464 1.00 74.97 S ATOM 53905 SG CYS H 51 62.764 45.469 71.249 1.00 65.27 S ATOM 54753 SG CYS I 18 39.499 59.797 75.697 1.00 53.83 S ATOM 54763 SG CYS I 19 36.581 57.926 73.672 1.00 49.15 S ATOM 56286 SG CYS I 122 37.297 56.595 77.111 1.00 47.39 S Time building chain proxies: 21.07, per 1000 atoms: 0.33 Number of scatterers: 63435 At special positions: 0 Unit cell: (128.877, 172.197, 200.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 114 16.00 P 143 15.00 Mg 1 11.99 O 6473 8.00 N 5779 7.00 C 19778 6.00 H 31140 1.00 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 - 3.50 Amino acid : False - 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: 39.52 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 H 101 " pdb="FE1 SF4 H 101 " - pdb=" SG CYS H 25 " pdb="FE2 SF4 H 101 " - pdb=" SG CYS H 48 " pdb="FE4 SF4 H 101 " - pdb=" SG CYS H 51 " pdb="FE3 SF4 H 101 " - pdb=" SG CYS H 57 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 972 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 886 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 969 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 962 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 122 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 18 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 19 " Number of angles added : 12 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 34 sheets defined 37.9% alpha, 10.1% beta 66 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 27.44 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.560A pdb=" N ILE A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 204 through 225 removed outlier: 4.027A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.835A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.575A pdb=" N ALA B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.785A pdb=" N ARG B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 267 " --> pdb=" O CYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.119A pdb=" N LYS B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 4.352A pdb=" N SER C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 250 through 256 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 305 Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 338 through 353 Processing helix chain 'C' and resid 384 through 409 removed outlier: 3.637A pdb=" N ARG C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 594 through 596 No H-bonds generated for 'chain 'C' and resid 594 through 596' Processing helix chain 'C' and resid 600 through 602 No H-bonds generated for 'chain 'C' and resid 600 through 602' Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 634 through 640 Processing helix chain 'C' and resid 743 through 746 No H-bonds generated for 'chain 'C' and resid 743 through 746' Processing helix chain 'C' and resid 781 through 783 No H-bonds generated for 'chain 'C' and resid 781 through 783' Processing helix chain 'C' and resid 819 through 828 Processing helix chain 'C' and resid 858 through 860 No H-bonds generated for 'chain 'C' and resid 858 through 860' Processing helix chain 'C' and resid 922 through 926 Proline residue: C 926 - end of helix Processing helix chain 'C' and resid 932 through 945 Processing helix chain 'C' and resid 955 through 961 removed outlier: 3.836A pdb=" N ARG C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 960 " --> pdb=" O TRP C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 992 removed outlier: 4.035A pdb=" N ASN C 992 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1084 through 1092 Processing helix chain 'C' and resid 1098 through 1110 removed outlier: 4.315A pdb=" N VAL C1102 " --> pdb=" O VAL C1098 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C1103 " --> pdb=" O THR C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1132 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.204A pdb=" N LYS D 108 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 183 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 191 through 227 removed outlier: 5.027A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 287 through 304 removed outlier: 3.556A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 341 through 360 Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 462 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 482 through 490 removed outlier: 3.784A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 529 through 532 No H-bonds generated for 'chain 'D' and resid 529 through 532' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 607 through 615 Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 686 through 698 Processing helix chain 'D' and resid 701 through 720 Processing helix chain 'D' and resid 737 through 757 Processing helix chain 'D' and resid 762 through 787 Processing helix chain 'D' and resid 793 through 799 Processing helix chain 'D' and resid 806 through 812 Processing helix chain 'D' and resid 841 through 875 removed outlier: 3.882A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA D 863 " --> pdb=" O ALA D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 949 Processing helix chain 'D' and resid 959 through 961 No H-bonds generated for 'chain 'D' and resid 959 through 961' Processing helix chain 'D' and resid 970 through 973 No H-bonds generated for 'chain 'D' and resid 970 through 973' Processing helix chain 'D' and resid 989 through 1002 Proline residue: D1000 - end of helix Processing helix chain 'D' and resid 1023 through 1030 Processing helix chain 'D' and resid 1101 through 1128 removed outlier: 7.829A pdb=" N GLN D1110 " --> pdb=" O ARG D1106 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N ARG D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA D1112 " --> pdb=" O LEU D1108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D1113 " --> pdb=" O GLY D1109 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1145 removed outlier: 3.705A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1177 Processing helix chain 'D' and resid 1193 through 1198 Processing helix chain 'D' and resid 1203 through 1209 Processing helix chain 'D' and resid 1212 through 1222 removed outlier: 3.743A pdb=" N ILE D1221 " --> pdb=" O THR D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1231 through 1237 Processing helix chain 'D' and resid 1244 through 1246 No H-bonds generated for 'chain 'D' and resid 1244 through 1246' Processing helix chain 'D' and resid 1259 through 1264 removed outlier: 3.547A pdb=" N ALA D1264 " --> pdb=" O GLU D1260 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.534A pdb=" N GLU E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 removed outlier: 3.601A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 77 Processing helix chain 'F' and resid 218 through 226 Processing helix chain 'F' and resid 234 through 255 Processing helix chain 'F' and resid 262 through 297 removed outlier: 4.958A pdb=" N ARG F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 320 Processing helix chain 'F' and resid 330 through 349 Processing helix chain 'F' and resid 357 through 377 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 394 through 403 Processing helix chain 'F' and resid 434 through 453 removed outlier: 3.689A pdb=" N THR F 453 " --> pdb=" O SER F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 466 Processing helix chain 'F' and resid 476 through 483 Processing helix chain 'F' and resid 487 through 501 Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 92 through 107 Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 24 through 27 Processing helix chain 'H' and resid 30 through 33 removed outlier: 3.733A pdb=" N PHE H 33 " --> pdb=" O PRO H 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 30 through 33' Processing helix chain 'H' and resid 42 through 50 removed outlier: 4.002A pdb=" N ALA H 50 " --> pdb=" O LYS H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'I' and resid 2 through 11 Processing helix chain 'I' and resid 17 through 30 Processing helix chain 'I' and resid 52 through 64 Processing helix chain 'I' and resid 92 through 99 Processing helix chain 'I' and resid 121 through 134 Processing helix chain 'I' and resid 154 through 167 removed outlier: 3.505A pdb=" N LEU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'I' and resid 257 through 268 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 287 through 302 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.470A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.000A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.516A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 85 through 87 Processing sheet with id= F, first strand: chain 'B' and resid 93 through 97 removed outlier: 3.976A pdb=" N SER B 53 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= H, first strand: chain 'C' and resid 108 through 113 Processing sheet with id= I, first strand: chain 'C' and resid 135 through 137 Processing sheet with id= J, first strand: chain 'C' and resid 171 through 173 Processing sheet with id= K, first strand: chain 'C' and resid 183 through 186 Processing sheet with id= L, first strand: chain 'C' and resid 189 through 196 removed outlier: 3.689A pdb=" N LEU C 217 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 457 through 459 Processing sheet with id= N, first strand: chain 'C' and resid 531 through 534 Processing sheet with id= O, first strand: chain 'C' and resid 562 through 565 Processing sheet with id= P, first strand: chain 'C' and resid 670 through 674 removed outlier: 5.943A pdb=" N ALA C 664 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL C 653 " --> pdb=" O ALA C 664 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1027 through 1033 removed outlier: 6.686A pdb=" N ILE C 918 " --> pdb=" O ALA C 725 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 809 through 811 Processing sheet with id= S, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= T, first strand: chain 'C' and resid 738 through 741 removed outlier: 7.479A pdb=" N LEU C 740 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE C 901 " --> pdb=" O LEU C 740 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 752 through 763 removed outlier: 3.775A pdb=" N GLY C 852 " --> pdb=" O TYR C 875 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 877 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE C 850 " --> pdb=" O ALA C 877 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= W, first strand: chain 'D' and resid 425 through 429 Processing sheet with id= X, first strand: chain 'D' and resid 430 through 432 removed outlier: 5.929A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 625 through 628 Processing sheet with id= Z, first strand: chain 'D' and resid 892 through 895 Processing sheet with id= AA, first strand: chain 'D' and resid 1046 through 1053 removed outlier: 3.541A pdb=" N LYS D1058 " --> pdb=" O GLU D1051 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D1053 " --> pdb=" O THR D1056 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D1056 " --> pdb=" O THR D1053 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id= AC, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.247A pdb=" N ASP D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 924 through 926 removed outlier: 3.952A pdb=" N ALA D 932 " --> pdb=" O VAL D 924 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL D 926 " --> pdb=" O VAL D 930 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL D 930 " --> pdb=" O VAL D 926 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 27 through 33 Processing sheet with id= AF, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.550A pdb=" N ILE G 61 " --> pdb=" O CYS G 56 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 32 through 34 Processing sheet with id= AH, first strand: chain 'I' and resid 172 through 176 1096 hydrogen bonds defined for protein. 3174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 23.07 Time building geometry restraints manager: 41.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 31127 1.13 - 1.41: 13184 1.41 - 1.70: 19735 1.70 - 1.99: 192 1.99 - 2.28: 12 Bond restraints: 64250 Sorted by residual: bond pdb=" N4 DC Q 12 " pdb=" H42 DC Q 12 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" N4 DC Q 12 " pdb=" H41 DC Q 12 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" C5 DC Q 12 " pdb=" H5 DC Q 12 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C6 DC Q 12 " pdb=" H6 DC Q 12 " ideal model delta sigma weight residual 0.930 1.077 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C3' DC Q 12 " pdb=" H3' DC Q 12 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 64245 not shown) Histogram of bond angle deviations from ideal: 73.62 - 85.72: 15 85.72 - 97.82: 0 97.82 - 109.92: 52653 109.92 - 122.02: 52946 122.02 - 134.12: 10896 Bond angle restraints: 116510 Sorted by residual: angle pdb=" C LEU B 60 " pdb=" CA LEU B 60 " pdb=" HA LEU B 60 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB LEU B 60 " pdb=" CA LEU B 60 " pdb=" HA LEU B 60 " ideal model delta sigma weight residual 109.00 74.06 34.94 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" HA LEU B 60 " ideal model delta sigma weight residual 110.00 77.99 32.01 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C3' DC Q 21 " pdb=" O3' DC Q 21 " pdb=" P DG Q 22 " ideal model delta sigma weight residual 120.20 104.38 15.82 1.50e+00 4.44e-01 1.11e+02 angle pdb=" C3' DT Q 16 " pdb=" O3' DT Q 16 " pdb=" P DC Q 17 " ideal model delta sigma weight residual 120.20 104.62 15.58 1.50e+00 4.44e-01 1.08e+02 ... (remaining 116505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 27972 35.28 - 70.55: 1280 70.55 - 105.83: 22 105.83 - 141.11: 1 141.11 - 176.38: 4 Dihedral angle restraints: 29279 sinusoidal: 17303 harmonic: 11976 Sorted by residual: dihedral pdb=" CA ARG I 83 " pdb=" C ARG I 83 " pdb=" N PHE I 84 " pdb=" CA PHE I 84 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" C LEU B 60 " pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" CB LEU B 60 " ideal model delta harmonic sigma weight residual -122.60 -134.42 11.82 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" CA PRO D 641 " pdb=" C PRO D 641 " pdb=" N PRO D 642 " pdb=" CA PRO D 642 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 29276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4991 0.104 - 0.209: 163 0.209 - 0.313: 0 0.313 - 0.418: 3 0.418 - 0.522: 5 Chirality restraints: 5162 Sorted by residual: chirality pdb=" P DC Q 12 " pdb=" OP1 DC Q 12 " pdb=" OP2 DC Q 12 " pdb=" O5' DC Q 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" P DC Q 21 " pdb=" OP1 DC Q 21 " pdb=" OP2 DC Q 21 " pdb=" O5' DC Q 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" P DG Q 22 " pdb=" OP1 DG Q 22 " pdb=" OP2 DG Q 22 " pdb=" O5' DG Q 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 5159 not shown) Planarity restraints: 9151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C1142 " 0.025 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C SER C1142 " -0.084 2.00e-02 2.50e+03 pdb=" O SER C1142 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP C1143 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 255 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO I 256 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 28 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N1 DC O 28 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DC O 28 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC O 28 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC O 28 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC O 28 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC O 28 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC O 28 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC O 28 " 0.006 2.00e-02 2.50e+03 pdb=" H5 DC O 28 " -0.004 2.00e-02 2.50e+03 pdb=" H6 DC O 28 " 0.003 2.00e-02 2.50e+03 ... (remaining 9148 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2019 2.15 - 2.76: 118172 2.76 - 3.37: 173590 3.37 - 3.99: 224471 3.99 - 4.60: 351575 Nonbonded interactions: 869827 Sorted by model distance: nonbonded pdb=" H ASN C 510 " pdb=" O PHE C 514 " model vdw 1.537 1.850 nonbonded pdb=" OE1 GLU H 43 " pdb=" H GLU H 43 " model vdw 1.572 1.850 nonbonded pdb=" O PRO D 434 " pdb=" HZ3 LYS D 712 " model vdw 1.583 1.850 nonbonded pdb=" O THR C 491 " pdb="HD21 ASN C 613 " model vdw 1.584 1.850 nonbonded pdb=" OD1 ASP D 626 " pdb=" HE ARG D 660 " model vdw 1.586 1.850 ... (remaining 869822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.220 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: 0.870 Extract box with map and model: 8.950 Check model and map are aligned: 0.720 Set scattering table: 0.490 Process input model: 208.770 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.003 0.058 33110 Z= 0.176 Angle : 0.521 15.818 45389 Z= 0.292 Chirality : 0.044 0.522 5162 Planarity : 0.003 0.049 5455 Dihedral : 17.511 176.384 12932 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3757 helix: 1.77 (0.14), residues: 1505 sheet: 0.05 (0.26), residues: 410 loop : -0.96 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 718 HIS 0.007 0.001 HIS D 505 PHE 0.019 0.001 PHE C 376 TYR 0.021 0.001 TYR E 32 ARG 0.005 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.8233 time to fit residues: 223.0171 Evaluate side-chains 143 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** I 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33110 Z= 0.303 Angle : 0.515 5.242 45389 Z= 0.284 Chirality : 0.042 0.372 5162 Planarity : 0.004 0.048 5455 Dihedral : 17.672 175.832 5678 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3757 helix: 1.63 (0.14), residues: 1518 sheet: -0.18 (0.25), residues: 442 loop : -1.03 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 773 HIS 0.008 0.001 HIS D 505 PHE 0.016 0.001 PHE C 376 TYR 0.018 0.001 TYR E 32 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8376 (t) cc_final: 0.8097 (t) outliers start: 4 outliers final: 2 residues processed: 147 average time/residue: 0.7545 time to fit residues: 186.5375 Evaluate side-chains 144 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 0.0670 chunk 290 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 347 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33110 Z= 0.234 Angle : 0.493 5.188 45389 Z= 0.273 Chirality : 0.041 0.374 5162 Planarity : 0.004 0.048 5455 Dihedral : 17.632 176.485 5678 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.26 % Allowed : 4.37 % Favored : 95.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3757 helix: 1.69 (0.14), residues: 1522 sheet: 0.01 (0.26), residues: 417 loop : -1.02 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.007 0.001 HIS D 505 PHE 0.016 0.001 PHE C 376 TYR 0.016 0.001 TYR E 32 ARG 0.003 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8369 (t) cc_final: 0.8089 (t) outliers start: 8 outliers final: 8 residues processed: 148 average time/residue: 0.7891 time to fit residues: 197.1644 Evaluate side-chains 151 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 372 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 333 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33110 Z= 0.329 Angle : 0.525 5.833 45389 Z= 0.290 Chirality : 0.042 0.377 5162 Planarity : 0.004 0.051 5455 Dihedral : 17.677 176.129 5678 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.48 % Allowed : 6.06 % Favored : 93.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3757 helix: 1.52 (0.14), residues: 1528 sheet: -0.22 (0.25), residues: 446 loop : -1.10 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 83 HIS 0.008 0.001 HIS D 505 PHE 0.016 0.001 PHE C 909 TYR 0.016 0.001 TYR E 32 ARG 0.003 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8389 (t) cc_final: 0.8115 (t) outliers start: 15 outliers final: 9 residues processed: 155 average time/residue: 0.7734 time to fit residues: 200.5743 Evaluate side-chains 152 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33110 Z= 0.311 Angle : 0.522 5.746 45389 Z= 0.288 Chirality : 0.042 0.393 5162 Planarity : 0.004 0.050 5455 Dihedral : 17.697 176.365 5678 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.54 % Allowed : 7.08 % Favored : 92.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3757 helix: 1.51 (0.14), residues: 1527 sheet: -0.21 (0.25), residues: 446 loop : -1.10 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 83 HIS 0.008 0.001 HIS D 505 PHE 0.015 0.001 PHE C 376 TYR 0.016 0.001 TYR E 32 ARG 0.003 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8394 (t) cc_final: 0.8121 (t) outliers start: 17 outliers final: 12 residues processed: 154 average time/residue: 0.7790 time to fit residues: 202.6667 Evaluate side-chains 153 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 1.9990 chunk 335 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 372 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33110 Z= 0.181 Angle : 0.485 6.332 45389 Z= 0.269 Chirality : 0.040 0.387 5162 Planarity : 0.003 0.049 5455 Dihedral : 17.669 177.181 5678 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.38 % Allowed : 7.78 % Favored : 91.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3757 helix: 1.70 (0.14), residues: 1534 sheet: 0.03 (0.26), residues: 417 loop : -0.99 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 83 HIS 0.005 0.001 HIS D 505 PHE 0.012 0.001 PHE F 249 TYR 0.011 0.001 TYR E 32 ARG 0.001 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8371 (t) cc_final: 0.8097 (t) outliers start: 12 outliers final: 12 residues processed: 150 average time/residue: 0.7926 time to fit residues: 199.0820 Evaluate side-chains 152 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 313 optimal weight: 0.5980 chunk 208 optimal weight: 0.6980 chunk 371 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33110 Z= 0.233 Angle : 0.492 5.445 45389 Z= 0.272 Chirality : 0.041 0.388 5162 Planarity : 0.004 0.050 5455 Dihedral : 17.669 177.348 5678 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.51 % Allowed : 8.04 % Favored : 91.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3757 helix: 1.69 (0.14), residues: 1534 sheet: -0.06 (0.26), residues: 432 loop : -1.03 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.006 0.001 HIS D 505 PHE 0.013 0.001 PHE F 249 TYR 0.012 0.001 TYR E 32 ARG 0.002 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8374 (t) cc_final: 0.8097 (t) outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.7485 time to fit residues: 191.7279 Evaluate side-chains 153 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 221 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 183 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33110 Z= 0.239 Angle : 0.494 7.932 45389 Z= 0.273 Chirality : 0.041 0.391 5162 Planarity : 0.004 0.049 5455 Dihedral : 17.671 177.521 5678 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.48 % Allowed : 8.35 % Favored : 91.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3757 helix: 1.70 (0.14), residues: 1533 sheet: -0.05 (0.26), residues: 432 loop : -1.02 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.006 0.001 HIS D 505 PHE 0.024 0.001 PHE C 257 TYR 0.012 0.001 TYR A 168 ARG 0.002 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8376 (t) cc_final: 0.8105 (t) outliers start: 15 outliers final: 13 residues processed: 152 average time/residue: 0.7818 time to fit residues: 200.6479 Evaluate side-chains 152 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 345 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 327 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33110 Z= 0.258 Angle : 0.503 7.542 45389 Z= 0.278 Chirality : 0.041 0.390 5162 Planarity : 0.004 0.051 5455 Dihedral : 17.680 177.602 5678 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.51 % Allowed : 8.51 % Favored : 90.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3757 helix: 1.67 (0.14), residues: 1531 sheet: -0.08 (0.25), residues: 433 loop : -1.04 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 83 HIS 0.006 0.001 HIS D 505 PHE 0.022 0.001 PHE C 257 TYR 0.016 0.001 TYR C 283 ARG 0.002 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8377 (t) cc_final: 0.8100 (t) outliers start: 16 outliers final: 14 residues processed: 151 average time/residue: 0.7883 time to fit residues: 200.8777 Evaluate side-chains 153 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.9980 chunk 365 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 383 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33110 Z= 0.309 Angle : 0.519 8.176 45389 Z= 0.286 Chirality : 0.042 0.392 5162 Planarity : 0.004 0.049 5455 Dihedral : 17.706 177.463 5678 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.48 % Allowed : 8.61 % Favored : 90.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3757 helix: 1.57 (0.14), residues: 1531 sheet: -0.18 (0.25), residues: 444 loop : -1.07 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 773 HIS 0.007 0.001 HIS D 505 PHE 0.020 0.001 PHE C 257 TYR 0.015 0.001 TYR C 283 ARG 0.003 0.000 ARG D 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8388 (t) cc_final: 0.8121 (t) REVERT: D 806 MET cc_start: 0.7915 (mmt) cc_final: 0.7527 (mmt) outliers start: 15 outliers final: 15 residues processed: 149 average time/residue: 0.7686 time to fit residues: 192.9284 Evaluate side-chains 155 residues out of total 3149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 614 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 815 MET Chi-restraints excluded: chain D residue 1191 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 0.6980 chunk 325 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 84 optimal weight: 0.0040 chunk 305 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 314 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.122779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080790 restraints weight = 174606.878| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.54 r_work: 0.3099 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33110 Z= 0.218 Angle : 0.493 8.060 45389 Z= 0.273 Chirality : 0.041 0.392 5162 Planarity : 0.004 0.050 5455 Dihedral : 17.695 177.926 5678 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.51 % Allowed : 8.67 % Favored : 90.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3757 helix: 1.68 (0.14), residues: 1528 sheet: 0.02 (0.26), residues: 416 loop : -1.01 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.005 0.001 HIS D 505 PHE 0.017 0.001 PHE C 257 TYR 0.015 0.001 TYR C 283 ARG 0.008 0.000 ARG I 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9231.83 seconds wall clock time: 161 minutes 20.75 seconds (9680.75 seconds total)