Starting phenix.real_space_refine on Wed Jan 15 03:23:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7b_23210/01_2025/7l7b_23210_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7b_23210/01_2025/7l7b_23210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l7b_23210/01_2025/7l7b_23210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7b_23210/01_2025/7l7b_23210.map" model { file = "/net/cci-nas-00/data/ceres_data/7l7b_23210/01_2025/7l7b_23210_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7b_23210/01_2025/7l7b_23210_neut_trim.cif" } resolution = 3.26 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= 0.020 sd= 0.120 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 88 5.16 5 Cl 2 4.86 5 C 15596 2.51 5 N 4256 2.21 5 O 4778 1.98 5 H 25027 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 49750 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3482 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212} Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3688 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 225} Chain: "C" Number of atoms: 18442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 18442 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 49, 'TRANS': 1116} Chain: "D" Number of atoms: 18266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 18266 Classifications: {'peptide': 1148} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1101} Chain breaks: 1 Chain: "E" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1279 Classifications: {'peptide': 78} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4487 Classifications: {'peptide': 272} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 258} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 1, ' ZN': 2, 'FI8': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38253 SG CYS D 790 37.931 98.935 89.757 1.00101.42 S ATOM 39409 SG CYS D 864 40.535 96.539 88.684 1.00100.07 S ATOM 39509 SG CYS D 871 40.214 98.274 91.810 1.00 95.85 S ATOM 39552 SG CYS D 874 37.576 96.119 91.434 1.00100.42 S ATOM 26572 SG CYS D 60 99.102 106.863 64.018 1.00130.49 S ATOM 26599 SG CYS D 62 100.503 106.459 61.132 1.00132.98 S ATOM 26829 SG CYS D 75 99.099 109.502 61.473 1.00136.11 S ATOM 26875 SG CYS D 78 97.250 106.048 60.636 1.00132.03 S Time building chain proxies: 17.16, per 1000 atoms: 0.34 Number of scatterers: 49750 At special positions: 0 Unit cell: (134.292, 134.292, 180.861, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 88 16.00 Mg 1 11.99 O 4778 8.00 N 4256 7.00 C 15596 6.00 H 25027 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 - 3.00 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: 10.10 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 874 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 864 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 790 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 871 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " Number of angles added : 12 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 39 sheets defined 40.9% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 4.226A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.663A pdb=" N LEU A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.552A pdb=" N ASN A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.892A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.583A pdb=" N ILE B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 223 removed outlier: 3.702A pdb=" N GLY B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 51 removed outlier: 3.525A pdb=" N VAL C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.670A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 202 through 211 removed outlier: 3.950A pdb=" N LEU C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 removed outlier: 4.079A pdb=" N ALA C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 4.260A pdb=" N LEU C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.768A pdb=" N ASN C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'C' and resid 279 through 285 removed outlier: 3.776A pdb=" N ARG C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 376 through 387 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 397 through 411 removed outlier: 3.771A pdb=" N ILE C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 431 through 458 removed outlier: 4.200A pdb=" N THR C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.721A pdb=" N LEU C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 483 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 585 through 592 removed outlier: 3.639A pdb=" N PHE C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 649 through 653 removed outlier: 3.586A pdb=" N ASP C 653 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 665 Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 683 through 691 removed outlier: 3.565A pdb=" N ALA C 687 " --> pdb=" O ILE C 683 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 830 through 835 removed outlier: 3.542A pdb=" N ILE C 834 " --> pdb=" O ASP C 831 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 835 " --> pdb=" O SER C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 879 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.574A pdb=" N ASP C 956 " --> pdb=" O PRO C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 973 No H-bonds generated for 'chain 'C' and resid 971 through 973' Processing helix chain 'C' and resid 974 through 979 Processing helix chain 'C' and resid 980 through 997 removed outlier: 4.463A pdb=" N VAL C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1021 Processing helix chain 'C' and resid 1056 through 1060 removed outlier: 3.792A pdb=" N LYS C1060 " --> pdb=" O VAL C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1100 removed outlier: 3.676A pdb=" N VAL C1093 " --> pdb=" O GLY C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1111 removed outlier: 3.548A pdb=" N LEU C1105 " --> pdb=" O ALA C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1129 removed outlier: 3.549A pdb=" N GLU C1124 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C1125 " --> pdb=" O ARG C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 removed outlier: 4.098A pdb=" N LYS C1142 " --> pdb=" O PRO C1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.531A pdb=" N VAL D 87 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.635A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 151 through 162 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 184 through 198 removed outlier: 3.585A pdb=" N SER D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 219 removed outlier: 3.679A pdb=" N VAL D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.865A pdb=" N TRP D 225 " --> pdb=" O LYS D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 275 removed outlier: 4.273A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.526A pdb=" N LEU D 320 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.504A pdb=" N VAL D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.797A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.760A pdb=" N ASN D 478 " --> pdb=" O SER D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 502 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.688A pdb=" N ASN D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 588 through 603 Processing helix chain 'D' and resid 611 through 627 removed outlier: 3.602A pdb=" N LYS D 616 " --> pdb=" O LEU D 612 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 661 removed outlier: 4.425A pdb=" N TYR D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 691 Processing helix chain 'D' and resid 696 through 704 removed outlier: 3.723A pdb=" N SER D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 717 Processing helix chain 'D' and resid 744 through 780 removed outlier: 4.585A pdb=" N LYS D 757 " --> pdb=" O HIS D 753 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY D 758 " --> pdb=" O GLY D 754 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 759 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 851 Processing helix chain 'D' and resid 860 through 864 Processing helix chain 'D' and resid 871 through 876 Processing helix chain 'D' and resid 890 through 901 removed outlier: 3.921A pdb=" N ILE D 894 " --> pdb=" O ALA D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 907 Processing helix chain 'D' and resid 924 through 933 removed outlier: 3.572A pdb=" N GLU D 933 " --> pdb=" O GLU D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1009 removed outlier: 3.841A pdb=" N ARG D1007 " --> pdb=" O HIS D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1028 removed outlier: 3.531A pdb=" N LEU D1028 " --> pdb=" O ARG D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1046 removed outlier: 4.355A pdb=" N ILE D1038 " --> pdb=" O ASN D1034 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1076 removed outlier: 4.131A pdb=" N ASP D1076 " --> pdb=" O GLU D1072 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1079 No H-bonds generated for 'chain 'D' and resid 1077 through 1079' Processing helix chain 'D' and resid 1093 through 1098 Processing helix chain 'D' and resid 1103 through 1108 Processing helix chain 'D' and resid 1112 through 1122 removed outlier: 3.556A pdb=" N VAL D1116 " --> pdb=" O GLU D1112 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D1122 " --> pdb=" O THR D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1139 Processing helix chain 'D' and resid 1144 through 1147 Processing helix chain 'D' and resid 1148 through 1153 removed outlier: 3.598A pdb=" N ARG D1152 " --> pdb=" O MET D1148 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 4.380A pdb=" N ASP E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 77 removed outlier: 4.003A pdb=" N HIS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.694A pdb=" N ILE F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 144 removed outlier: 4.273A pdb=" N GLU F 139 " --> pdb=" O HIS F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 170 removed outlier: 3.840A pdb=" N LYS F 152 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.886A pdb=" N LEU F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 220 removed outlier: 3.975A pdb=" N THR F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 251 Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 266 through 278 removed outlier: 3.650A pdb=" N GLN F 278 " --> pdb=" O MET F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 325 removed outlier: 3.742A pdb=" N ALA F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 340 Processing helix chain 'F' and resid 348 through 357 removed outlier: 3.756A pdb=" N PHE F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 376 removed outlier: 3.801A pdb=" N HIS F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 385 removed outlier: 5.445A pdb=" N LYS F 382 " --> pdb=" O SER F 378 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 383 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.549A pdb=" N LYS A 8 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 26 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 10 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 24 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS A 22 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 198 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 24 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 196 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU A 26 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 194 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 175 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102 removed outlier: 3.502A pdb=" N GLU A 139 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 55 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 53 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 145 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.011A pdb=" N ILE B 4 " --> pdb=" O ILE B 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.634A pdb=" N GLU B 197 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 10 Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 102 removed outlier: 3.861A pdb=" N ALA B 55 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 143 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 53 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY B 145 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL B 51 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 56 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.977A pdb=" N ALA B 128 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.519A pdb=" N VAL B 149 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.557A pdb=" N HIS C 3 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 14 " --> pdb=" O HIS C 3 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA C1001 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N MET C 13 " --> pdb=" O ALA C1001 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 92 removed outlier: 4.059A pdb=" N GLY C 113 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB5, first strand: chain 'C' and resid 135 through 136 removed outlier: 6.779A pdb=" N SER C 135 " --> pdb=" O SER C 507 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 145 removed outlier: 4.183A pdb=" N ILE C 162 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 173 removed outlier: 4.025A pdb=" N GLU C 170 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.796A pdb=" N LYS C 287 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 293 through 294 removed outlier: 3.697A pdb=" N VAL C 303 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 328 Processing sheet with id=AC3, first strand: chain 'C' and resid 342 through 343 Processing sheet with id=AC4, first strand: chain 'C' and resid 556 through 557 removed outlier: 5.446A pdb=" N GLU C 580 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP C 571 " --> pdb=" O THR C 578 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR C 578 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC6, first strand: chain 'C' and resid 612 through 614 Processing sheet with id=AC7, first strand: chain 'C' and resid 720 through 724 removed outlier: 7.133A pdb=" N GLU C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL C 706 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 712 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 740 through 741 Processing sheet with id=AC9, first strand: chain 'C' and resid 948 through 952 removed outlier: 7.589A pdb=" N ILE C 788 " --> pdb=" O SER C 949 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 951 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE C 790 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 789 " --> pdb=" O ILE C 969 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ILE C 968 " --> pdb=" O ASN C 771 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 773 " --> pdb=" O ILE C 968 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 803 through 810 removed outlier: 3.856A pdb=" N VAL C 922 " --> pdb=" O CYS C 810 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP C 902 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA C 927 " --> pdb=" O ILE C 900 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE C 900 " --> pdb=" O ALA C 927 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 859 through 861 Processing sheet with id=AD3, first strand: chain 'C' and resid 1062 through 1063 removed outlier: 3.513A pdb=" N PHE D 426 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS D 355 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL D 431 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU D 357 " --> pdb=" O VAL D 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1062 through 1063 removed outlier: 7.455A pdb=" N ILE D 436 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL D 343 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU D 438 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 345 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1164 through 1165 removed outlier: 4.468A pdb=" N VAL C1157 " --> pdb=" O ILE C1165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.581A pdb=" N LEU D 97 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASP D 229 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N ALA D 99 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE D 227 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 241 through 244 removed outlier: 3.728A pdb=" N LEU D 244 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE D 249 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 537 through 543 Processing sheet with id=AD9, first strand: chain 'D' and resid 796 through 798 removed outlier: 3.869A pdb=" N ILE D 856 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 971 through 974 Processing sheet with id=AE2, first strand: chain 'D' and resid 1064 through 1065 removed outlier: 3.523A pdb=" N GLU D1065 " --> pdb=" O VAL D1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1156 through 1157 938 hydrogen bonds defined for protein. 2622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.85 Time building geometry restraints manager: 12.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25005 1.02 - 1.22: 46 1.22 - 1.42: 9961 1.42 - 1.62: 14945 1.62 - 1.83: 149 Bond restraints: 50106 Sorted by residual: bond pdb=" C LEU D 418 " pdb=" O LEU D 418 " ideal model delta sigma weight residual 1.237 1.106 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C PRO D 416 " pdb=" O PRO D 416 " ideal model delta sigma weight residual 1.235 1.157 0.078 7.90e-03 1.60e+04 9.69e+01 bond pdb=" C HIS D 419 " pdb=" O HIS D 419 " ideal model delta sigma weight residual 1.235 1.128 0.107 1.26e-02 6.30e+03 7.18e+01 bond pdb=" CA LEU D 418 " pdb=" C LEU D 418 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.30e-02 5.92e+03 7.01e+01 bond pdb=" C VAL C1143 " pdb=" N LEU C1144 " ideal model delta sigma weight residual 1.335 1.231 0.104 1.31e-02 5.83e+03 6.30e+01 ... (remaining 50101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 90420 2.47 - 4.95: 569 4.95 - 7.42: 54 7.42 - 9.90: 13 9.90 - 12.37: 2 Bond angle restraints: 91058 Sorted by residual: angle pdb=" CA PRO D 416 " pdb=" C PRO D 416 " pdb=" N THR D 417 " ideal model delta sigma weight residual 116.09 125.28 -9.19 9.20e-01 1.18e+00 9.97e+01 angle pdb=" CA PRO D 416 " pdb=" C PRO D 416 " pdb=" O PRO D 416 " ideal model delta sigma weight residual 121.11 110.57 10.54 1.08e+00 8.57e-01 9.53e+01 angle pdb=" CA ALA D 415 " pdb=" C ALA D 415 " pdb=" N PRO D 416 " ideal model delta sigma weight residual 120.52 126.55 -6.03 8.30e-01 1.45e+00 5.27e+01 angle pdb=" CA LEU D 418 " pdb=" C LEU D 418 " pdb=" O LEU D 418 " ideal model delta sigma weight residual 120.55 113.33 7.22 1.06e+00 8.90e-01 4.64e+01 angle pdb=" C SER C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta sigma weight residual 119.76 113.55 6.21 1.00e+00 1.00e+00 3.85e+01 ... (remaining 91053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 22507 31.38 - 62.76: 719 62.76 - 94.14: 23 94.14 - 125.52: 1 125.52 - 156.90: 4 Dihedral angle restraints: 23254 sinusoidal: 13194 harmonic: 10060 Sorted by residual: dihedral pdb=" CA GLU D 582 " pdb=" C GLU D 582 " pdb=" N VAL D 583 " pdb=" CA VAL D 583 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLN B 187 " pdb=" C GLN B 187 " pdb=" N LYS B 188 " pdb=" CA LYS B 188 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU D 505 " pdb=" C GLU D 505 " pdb=" N ALA D 506 " pdb=" CA ALA D 506 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 23251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3846 0.142 - 0.284: 18 0.284 - 0.426: 3 0.426 - 0.567: 2 0.567 - 0.709: 1 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CA HIS D 419 " pdb=" N HIS D 419 " pdb=" C HIS D 419 " pdb=" CB HIS D 419 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CB THR D 417 " pdb=" CA THR D 417 " pdb=" OG1 THR D 417 " pdb=" CG2 THR D 417 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA LEU D 418 " pdb=" N LEU D 418 " pdb=" C LEU D 418 " pdb=" CB LEU D 418 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 3867 not shown) Planarity restraints: 7383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 453 " -0.045 2.00e-02 2.50e+03 8.84e-02 7.81e+01 pdb=" CG ASP D 453 " 0.153 2.00e-02 2.50e+03 pdb=" OD1 ASP D 453 " -0.059 2.00e-02 2.50e+03 pdb=" OD2 ASP D 453 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 401 " -0.033 2.00e-02 2.50e+03 6.32e-02 4.00e+01 pdb=" N ILE C 402 " 0.109 2.00e-02 2.50e+03 pdb=" CA ILE C 402 " -0.027 2.00e-02 2.50e+03 pdb=" H ILE C 402 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 413 " -0.030 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ASN D 413 " 0.104 2.00e-02 2.50e+03 pdb=" O ASN D 413 " -0.040 2.00e-02 2.50e+03 pdb=" N ARG D 414 " -0.035 2.00e-02 2.50e+03 ... (remaining 7380 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 789 2.10 - 2.72: 87379 2.72 - 3.35: 141355 3.35 - 3.97: 173936 3.97 - 4.60: 280235 Nonbonded interactions: 683694 Sorted by model distance: nonbonded pdb=" H THR E 65 " pdb=" OE2 GLU E 68 " model vdw 1.472 2.450 nonbonded pdb=" OE2 GLU C 291 " pdb="HD21 ASN C 326 " model vdw 1.500 2.450 nonbonded pdb="HD22 ASN C 744 " pdb=" OD2 ASP C 747 " model vdw 1.504 2.450 nonbonded pdb=" HH TYR C1069 " pdb=" OD2 ASP D 337 " model vdw 1.538 2.450 nonbonded pdb=" HG SER D1103 " pdb=" OE2 GLU D1134 " model vdw 1.540 2.450 ... (remaining 683689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 6 through 228)) } 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: 0.600 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: 0.660 Extract box with map and model: 1.510 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 93.750 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.120 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 25079 Z= 0.331 Angle : 0.717 12.369 33874 Z= 0.411 Chirality : 0.048 0.709 3870 Planarity : 0.005 0.088 4398 Dihedral : 12.892 156.896 9728 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 0.22 % Allowed : 0.52 % Favored : 99.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -1.34 (0.15), residues: 3111 helix: 0.71 (0.16), residues: 1087 sheet: -2.04 (0.29), residues: 309 loop : -1.78 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 998 HIS 0.022 0.001 HIS D 419 PHE 0.019 0.001 PHE D 579 TYR 0.036 0.001 TYR F 197 ARG 0.003 0.000 ARG C 872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 244 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LYS cc_start: 0.8966 (tttp) cc_final: 0.8620 (ttpp) REVERT: B 92 GLU cc_start: 0.7568 (tp30) cc_final: 0.7226 (tp30) REVERT: C 36 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 380 ILE cc_start: 0.7976 (mt) cc_final: 0.7531 (tp) REVERT: C 414 ASN cc_start: 0.8630 (m-40) cc_final: 0.8419 (p0) REVERT: C 480 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8036 (tp30) REVERT: C 1006 ASP cc_start: 0.8052 (t0) cc_final: 0.7784 (t0) REVERT: C 1147 GLU cc_start: 0.7762 (tp30) cc_final: 0.7536 (tp30) REVERT: D 59 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 319 MET cc_start: 0.8280 (mtp) cc_final: 0.8049 (mtp) REVERT: D 701 MET cc_start: 0.7644 (mtp) cc_final: 0.7301 (mtp) REVERT: D 867 ASN cc_start: 0.8503 (m110) cc_final: 0.8296 (m-40) REVERT: F 144 MET cc_start: 0.7832 (mmp) cc_final: 0.7456 (mmm) REVERT: F 170 TYR cc_start: 0.6947 (m-10) cc_final: 0.6732 (m-10) REVERT: F 263 MET cc_start: 0.6506 (ttm) cc_final: 0.6236 (ttp) REVERT: F 324 LEU cc_start: 0.7380 (tp) cc_final: 0.7031 (tt) outliers start: 6 outliers final: 3 residues processed: 249 average time/residue: 0.7225 time to fit residues: 277.7960 Evaluate side-chains 193 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1143 VAL Chi-restraints excluded: chain D residue 579 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 0.0870 chunk 129 optimal weight: 0.1980 chunk 80 optimal weight: 0.0570 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 596 GLN C1106 GLN D 221 ASN D 255 ASN D 878 ASN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081202 restraints weight = 109258.239| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.42 r_work: 0.2957 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25079 Z= 0.156 Angle : 0.547 6.660 33874 Z= 0.288 Chirality : 0.042 0.155 3870 Planarity : 0.004 0.083 4398 Dihedral : 6.903 139.298 3507 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 0.41 % Allowed : 4.07 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -1.11 (0.15), residues: 3111 helix: 0.85 (0.16), residues: 1117 sheet: -1.83 (0.29), residues: 312 loop : -1.67 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 998 HIS 0.007 0.001 HIS D 419 PHE 0.019 0.001 PHE D 166 TYR 0.013 0.001 TYR C 145 ARG 0.005 0.000 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 GLU cc_start: 0.7878 (tp30) cc_final: 0.7373 (tp30) REVERT: C 36 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 380 ILE cc_start: 0.7899 (mt) cc_final: 0.7542 (tp) REVERT: C 414 ASN cc_start: 0.8677 (m-40) cc_final: 0.8439 (p0) REVERT: C 480 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8118 (tp30) REVERT: C 747 ASP cc_start: 0.8582 (m-30) cc_final: 0.8261 (m-30) REVERT: C 1147 GLU cc_start: 0.8159 (tp30) cc_final: 0.7864 (tp30) REVERT: D 319 MET cc_start: 0.8708 (mtp) cc_final: 0.8419 (mtp) REVERT: D 867 ASN cc_start: 0.8743 (m110) cc_final: 0.8533 (m-40) REVERT: E 72 GLU cc_start: 0.7627 (tp30) cc_final: 0.7299 (tm-30) REVERT: F 144 MET cc_start: 0.7864 (mmp) cc_final: 0.7477 (mmm) REVERT: F 265 MET cc_start: 0.8146 (mtp) cc_final: 0.7930 (mtp) REVERT: F 324 LEU cc_start: 0.6889 (tp) cc_final: 0.6642 (tt) outliers start: 11 outliers final: 4 residues processed: 219 average time/residue: 0.7167 time to fit residues: 243.8536 Evaluate side-chains 195 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 553 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 149 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 151 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 ASN ** C 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN C1106 GLN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079746 restraints weight = 110465.821| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.46 r_work: 0.2925 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25079 Z= 0.183 Angle : 0.518 6.784 33874 Z= 0.272 Chirality : 0.042 0.149 3870 Planarity : 0.004 0.074 4398 Dihedral : 6.156 142.437 3504 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer: Outliers : 0.37 % Allowed : 5.77 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.97 (0.15), residues: 3111 helix: 1.01 (0.16), residues: 1121 sheet: -1.75 (0.28), residues: 326 loop : -1.63 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 998 HIS 0.006 0.001 HIS F 376 PHE 0.018 0.001 PHE D 166 TYR 0.015 0.001 TYR C 145 ARG 0.003 0.000 ARG D 775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 3.024 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: symmetry clash revert: symmetry clash REVERT: B 92 GLU cc_start: 0.7893 (tp30) cc_final: 0.7322 (tp30) REVERT: C 36 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 380 ILE cc_start: 0.8037 (mt) cc_final: 0.7718 (tp) REVERT: C 414 ASN cc_start: 0.8685 (m-40) cc_final: 0.8406 (p0) REVERT: C 480 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8040 (tp30) REVERT: C 492 ASP cc_start: 0.7674 (p0) cc_final: 0.7371 (p0) REVERT: C 938 MET cc_start: 0.9066 (mtm) cc_final: 0.8844 (mtp) REVERT: D 319 MET cc_start: 0.8724 (mtp) cc_final: 0.8416 (mtp) REVERT: D 1065 GLU cc_start: 0.7698 (pm20) cc_final: 0.7353 (pm20) REVERT: F 144 MET cc_start: 0.7885 (mmp) cc_final: 0.7499 (mmm) REVERT: F 263 MET cc_start: 0.6865 (ttp) cc_final: 0.6521 (ttp) REVERT: F 265 MET cc_start: 0.8348 (mtp) cc_final: 0.7938 (mtp) REVERT: F 324 LEU cc_start: 0.6896 (tp) cc_final: 0.6638 (tt) outliers start: 10 outliers final: 6 residues processed: 216 average time/residue: 0.7621 time to fit residues: 250.1807 Evaluate side-chains 199 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 193 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 201 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 596 GLN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 715 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.129608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078392 restraints weight = 110473.656| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.44 r_work: 0.2902 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25079 Z= 0.223 Angle : 0.523 6.580 33874 Z= 0.275 Chirality : 0.042 0.150 3870 Planarity : 0.004 0.068 4398 Dihedral : 6.045 143.079 3504 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 0.41 % Allowed : 7.29 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.94 (0.15), residues: 3111 helix: 1.02 (0.16), residues: 1134 sheet: -1.72 (0.28), residues: 325 loop : -1.62 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 998 HIS 0.006 0.001 HIS E 76 PHE 0.018 0.001 PHE D 166 TYR 0.015 0.001 TYR D 622 ARG 0.003 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 3.051 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: B 92 GLU cc_start: 0.7885 (tp30) cc_final: 0.7343 (tp30) REVERT: C 36 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 380 ILE cc_start: 0.8216 (mt) cc_final: 0.7937 (tp) REVERT: C 414 ASN cc_start: 0.8712 (m-40) cc_final: 0.8432 (p0) REVERT: C 480 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8150 (tp30) REVERT: C 938 MET cc_start: 0.9089 (mtm) cc_final: 0.8880 (mtp) REVERT: D 319 MET cc_start: 0.8709 (mtp) cc_final: 0.8444 (mtp) REVERT: D 640 GLU cc_start: 0.8801 (pp20) cc_final: 0.8485 (pp20) REVERT: D 701 MET cc_start: 0.7709 (mtp) cc_final: 0.7482 (mtp) REVERT: F 144 MET cc_start: 0.7904 (mmp) cc_final: 0.7542 (mmm) REVERT: F 324 LEU cc_start: 0.6923 (tp) cc_final: 0.6668 (tt) outliers start: 11 outliers final: 8 residues processed: 202 average time/residue: 0.7935 time to fit residues: 245.1712 Evaluate side-chains 195 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 282 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 288 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 596 GLN ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077945 restraints weight = 110125.349| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.41 r_work: 0.2896 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25079 Z= 0.211 Angle : 0.513 6.584 33874 Z= 0.269 Chirality : 0.042 0.151 3870 Planarity : 0.004 0.066 4398 Dihedral : 5.963 142.554 3504 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 0.44 % Allowed : 7.59 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.87 (0.15), residues: 3111 helix: 1.12 (0.16), residues: 1133 sheet: -1.74 (0.28), residues: 330 loop : -1.59 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.014 0.001 TYR D 622 ARG 0.004 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 3.044 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: symmetry clash REVERT: B 92 GLU cc_start: 0.7894 (tp30) cc_final: 0.7407 (tp30) REVERT: C 36 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 380 ILE cc_start: 0.8233 (mt) cc_final: 0.7975 (tp) REVERT: C 414 ASN cc_start: 0.8733 (m-40) cc_final: 0.8452 (p0) REVERT: C 480 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7986 (tp30) REVERT: D 186 GLN cc_start: 0.7492 (tm-30) cc_final: 0.7255 (tm-30) REVERT: D 319 MET cc_start: 0.8744 (mtp) cc_final: 0.8466 (mtp) REVERT: D 640 GLU cc_start: 0.8790 (pp20) cc_final: 0.8496 (pp20) REVERT: D 1065 GLU cc_start: 0.7608 (pm20) cc_final: 0.7335 (pm20) REVERT: F 144 MET cc_start: 0.7898 (mmp) cc_final: 0.7541 (mmm) REVERT: F 324 LEU cc_start: 0.6910 (tp) cc_final: 0.6655 (tt) outliers start: 12 outliers final: 8 residues processed: 199 average time/residue: 0.7607 time to fit residues: 232.2988 Evaluate side-chains 195 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 258 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 288 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN C 596 GLN ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS F 248 GLN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075443 restraints weight = 111257.240| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.42 r_work: 0.2853 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25079 Z= 0.321 Angle : 0.556 7.033 33874 Z= 0.294 Chirality : 0.043 0.157 3870 Planarity : 0.004 0.064 4398 Dihedral : 6.129 142.970 3503 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.26 % Favored : 91.71 % Rotamer: Outliers : 0.67 % Allowed : 8.48 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.00 (0.15), residues: 3111 helix: 1.02 (0.16), residues: 1129 sheet: -1.77 (0.29), residues: 324 loop : -1.69 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.020 0.001 PHE D 166 TYR 0.019 0.001 TYR D 622 ARG 0.003 0.000 ARG C 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 3.108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7454 (pt) REVERT: B 92 GLU cc_start: 0.7917 (tp30) cc_final: 0.7425 (tp30) REVERT: C 36 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 380 ILE cc_start: 0.8258 (mt) cc_final: 0.8038 (tp) REVERT: C 414 ASN cc_start: 0.8711 (m-40) cc_final: 0.8439 (p0) REVERT: C 480 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8091 (tp30) REVERT: D 83 THR cc_start: 0.8755 (t) cc_final: 0.8546 (m) REVERT: D 186 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7258 (tm-30) REVERT: D 319 MET cc_start: 0.8793 (mtp) cc_final: 0.8510 (mtp) REVERT: D 640 GLU cc_start: 0.8779 (pp20) cc_final: 0.8422 (pp20) REVERT: D 701 MET cc_start: 0.7642 (mtp) cc_final: 0.7134 (mtp) REVERT: F 144 MET cc_start: 0.7941 (mmp) cc_final: 0.7585 (mmm) REVERT: F 324 LEU cc_start: 0.6936 (tp) cc_final: 0.6700 (tt) outliers start: 18 outliers final: 13 residues processed: 209 average time/residue: 0.7770 time to fit residues: 250.3966 Evaluate side-chains 205 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 306 optimal weight: 10.0000 chunk 274 optimal weight: 0.0000 chunk 82 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 299 optimal weight: 0.0870 chunk 81 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 596 GLN ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078056 restraints weight = 109488.959| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.42 r_work: 0.2898 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25079 Z= 0.148 Angle : 0.503 7.331 33874 Z= 0.264 Chirality : 0.042 0.154 3870 Planarity : 0.004 0.065 4398 Dihedral : 5.929 141.946 3503 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 0.48 % Allowed : 9.18 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.78 (0.16), residues: 3111 helix: 1.23 (0.16), residues: 1127 sheet: -1.62 (0.29), residues: 325 loop : -1.57 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.021 0.001 PHE D 166 TYR 0.014 0.001 TYR C 145 ARG 0.002 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 3.084 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: symmetry clash REVERT: A 221 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7322 (pt) REVERT: B 92 GLU cc_start: 0.7910 (tp30) cc_final: 0.7641 (tp30) REVERT: C 36 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 380 ILE cc_start: 0.8255 (mt) cc_final: 0.8048 (tp) REVERT: C 414 ASN cc_start: 0.8710 (m-40) cc_final: 0.8439 (p0) REVERT: C 480 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7948 (tp30) REVERT: C 1014 MET cc_start: 0.7399 (mtt) cc_final: 0.7194 (mtt) REVERT: D 83 THR cc_start: 0.8601 (t) cc_final: 0.8376 (m) REVERT: D 107 PHE cc_start: 0.8506 (t80) cc_final: 0.8278 (t80) REVERT: D 186 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7175 (tm-30) REVERT: D 319 MET cc_start: 0.8743 (mtp) cc_final: 0.8436 (mtp) REVERT: D 640 GLU cc_start: 0.8780 (pp20) cc_final: 0.8498 (pp20) REVERT: D 701 MET cc_start: 0.7600 (mtp) cc_final: 0.7093 (mtp) REVERT: F 144 MET cc_start: 0.7932 (mmp) cc_final: 0.7575 (mmm) REVERT: F 248 GLN cc_start: 0.7439 (mt0) cc_final: 0.7157 (pp30) REVERT: F 324 LEU cc_start: 0.6883 (tp) cc_final: 0.6646 (tt) outliers start: 13 outliers final: 8 residues processed: 204 average time/residue: 0.7654 time to fit residues: 238.5177 Evaluate side-chains 200 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 664 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 212 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 206 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 GLN ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079319 restraints weight = 110095.022| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.44 r_work: 0.2917 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25079 Z= 0.143 Angle : 0.488 7.193 33874 Z= 0.255 Chirality : 0.041 0.149 3870 Planarity : 0.004 0.061 4398 Dihedral : 5.732 140.026 3503 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer: Outliers : 0.44 % Allowed : 9.36 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.62 (0.16), residues: 3111 helix: 1.38 (0.16), residues: 1129 sheet: -1.53 (0.29), residues: 319 loop : -1.51 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 998 HIS 0.007 0.001 HIS E 76 PHE 0.022 0.001 PHE D 166 TYR 0.013 0.001 TYR C 567 ARG 0.007 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 3.015 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 221 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7195 (pt) REVERT: B 72 LYS cc_start: 0.8941 (tttp) cc_final: 0.8611 (ttpp) REVERT: B 92 GLU cc_start: 0.7935 (tp30) cc_final: 0.7667 (tp30) REVERT: C 36 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 380 ILE cc_start: 0.8236 (mt) cc_final: 0.7987 (tp) REVERT: C 414 ASN cc_start: 0.8717 (m-40) cc_final: 0.8449 (p0) REVERT: C 480 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7952 (tp30) REVERT: C 1014 MET cc_start: 0.7396 (mtt) cc_final: 0.7161 (mtt) REVERT: D 186 GLN cc_start: 0.7414 (tm-30) cc_final: 0.7140 (tm-30) REVERT: D 319 MET cc_start: 0.8750 (mtp) cc_final: 0.8412 (mtp) REVERT: D 640 GLU cc_start: 0.8788 (pp20) cc_final: 0.8510 (pp20) REVERT: D 1065 GLU cc_start: 0.7438 (pm20) cc_final: 0.7189 (pm20) REVERT: F 144 MET cc_start: 0.7915 (mmp) cc_final: 0.7549 (mmm) REVERT: F 248 GLN cc_start: 0.7406 (mt0) cc_final: 0.7118 (pp30) REVERT: F 324 LEU cc_start: 0.6923 (tp) cc_final: 0.6691 (tt) outliers start: 12 outliers final: 7 residues processed: 211 average time/residue: 0.7878 time to fit residues: 257.0138 Evaluate side-chains 196 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 186 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 596 GLN ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.076516 restraints weight = 110194.132| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.40 r_work: 0.2873 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25079 Z= 0.273 Angle : 0.528 6.961 33874 Z= 0.278 Chirality : 0.042 0.150 3870 Planarity : 0.004 0.064 4398 Dihedral : 5.890 141.432 3503 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.19 % Rotamer: Outliers : 0.52 % Allowed : 9.62 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.72 (0.16), residues: 3111 helix: 1.29 (0.16), residues: 1128 sheet: -1.61 (0.29), residues: 327 loop : -1.54 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.033 0.001 PHE C 111 TYR 0.015 0.001 TYR D 622 ARG 0.007 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 3.101 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 221 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7288 (pt) REVERT: B 72 LYS cc_start: 0.8931 (tttp) cc_final: 0.8603 (ttpp) REVERT: B 92 GLU cc_start: 0.7945 (tp30) cc_final: 0.7656 (tp30) REVERT: C 36 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 380 ILE cc_start: 0.8203 (mt) cc_final: 0.7988 (tp) REVERT: C 414 ASN cc_start: 0.8735 (m-40) cc_final: 0.8459 (p0) REVERT: C 480 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8033 (tp30) REVERT: C 1014 MET cc_start: 0.7405 (mtt) cc_final: 0.7186 (mtt) REVERT: D 83 THR cc_start: 0.8660 (t) cc_final: 0.8444 (m) REVERT: D 186 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 319 MET cc_start: 0.8760 (mtp) cc_final: 0.8455 (mtp) REVERT: D 640 GLU cc_start: 0.8769 (pp20) cc_final: 0.8445 (pp20) REVERT: F 144 MET cc_start: 0.7945 (mmp) cc_final: 0.7589 (mmm) REVERT: F 324 LEU cc_start: 0.6868 (tp) cc_final: 0.6622 (tt) outliers start: 14 outliers final: 10 residues processed: 198 average time/residue: 0.7658 time to fit residues: 232.8047 Evaluate side-chains 196 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 1050 TYR Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 149 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 596 GLN ** C 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076964 restraints weight = 110085.672| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.40 r_work: 0.2881 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25079 Z= 0.228 Angle : 0.515 7.455 33874 Z= 0.270 Chirality : 0.042 0.152 3870 Planarity : 0.004 0.061 4398 Dihedral : 5.880 141.550 3503 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 0.48 % Allowed : 9.73 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.03 % 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: -0.70 (0.16), residues: 3111 helix: 1.28 (0.16), residues: 1130 sheet: -1.53 (0.29), residues: 323 loop : -1.53 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 998 HIS 0.008 0.001 HIS E 76 PHE 0.025 0.001 PHE C 111 TYR 0.013 0.001 TYR C 567 ARG 0.007 0.000 ARG E 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 3.075 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 221 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7256 (pt) REVERT: B 72 LYS cc_start: 0.8934 (tttp) cc_final: 0.8607 (ttpp) REVERT: B 92 GLU cc_start: 0.7958 (tp30) cc_final: 0.7665 (tp30) REVERT: C 36 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 414 ASN cc_start: 0.8744 (m-40) cc_final: 0.8464 (p0) REVERT: C 480 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8028 (tp30) REVERT: C 1014 MET cc_start: 0.7381 (mtt) cc_final: 0.7157 (mtt) REVERT: D 83 THR cc_start: 0.8657 (t) cc_final: 0.8440 (m) REVERT: D 186 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7175 (tm-30) REVERT: D 319 MET cc_start: 0.8747 (mtp) cc_final: 0.8444 (mtp) REVERT: D 640 GLU cc_start: 0.8768 (pp20) cc_final: 0.8471 (pp20) REVERT: D 701 MET cc_start: 0.7564 (mtp) cc_final: 0.7213 (mtp) REVERT: F 144 MET cc_start: 0.7933 (mmp) cc_final: 0.7580 (mmm) REVERT: F 324 LEU cc_start: 0.6916 (tp) cc_final: 0.6688 (tt) outliers start: 13 outliers final: 11 residues processed: 197 average time/residue: 0.8245 time to fit residues: 251.6116 Evaluate side-chains 197 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 1050 TYR Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 973 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7626 > 50: distance: 319 - 371: 17.727 distance: 336 - 392: 10.320 distance: 343 - 403: 12.138 distance: 352 - 371: 14.778 distance: 353 - 417: 10.149 distance: 371 - 372: 10.186 distance: 371 - 383: 23.782 distance: 372 - 373: 21.108 distance: 372 - 375: 15.693 distance: 372 - 384: 24.156 distance: 373 - 374: 8.756 distance: 373 - 392: 18.240 distance: 374 - 436: 20.852 distance: 375 - 376: 9.474 distance: 375 - 385: 25.491 distance: 375 - 386: 22.502 distance: 376 - 377: 21.820 distance: 376 - 378: 20.775 distance: 377 - 379: 11.887 distance: 377 - 387: 23.090 distance: 378 - 380: 5.089 distance: 378 - 388: 10.715 distance: 379 - 381: 14.421 distance: 379 - 389: 5.032 distance: 380 - 381: 7.899 distance: 380 - 390: 14.432 distance: 381 - 382: 7.762 distance: 382 - 391: 18.433 distance: 392 - 393: 7.977 distance: 392 - 398: 20.821 distance: 393 - 394: 8.195 distance: 393 - 396: 22.935 distance: 393 - 399: 18.591 distance: 394 - 395: 29.012 distance: 394 - 403: 17.169 distance: 395 - 443: 23.014 distance: 396 - 397: 12.664 distance: 396 - 400: 17.475 distance: 396 - 401: 14.124 distance: 397 - 402: 35.704 distance: 403 - 404: 7.470 distance: 403 - 410: 13.926 distance: 404 - 405: 14.914 distance: 404 - 407: 7.063 distance: 404 - 411: 11.273 distance: 405 - 406: 20.928 distance: 405 - 417: 5.534 distance: 407 - 408: 5.828 distance: 407 - 409: 6.650 distance: 407 - 412: 9.049 distance: 408 - 413: 41.831 distance: 409 - 414: 17.385 distance: 409 - 415: 26.272 distance: 409 - 416: 23.628 distance: 417 - 418: 13.968 distance: 417 - 425: 11.828 distance: 418 - 419: 14.153 distance: 418 - 421: 8.205 distance: 418 - 426: 10.458 distance: 419 - 420: 9.100 distance: 419 - 436: 15.341 distance: 421 - 422: 8.657 distance: 421 - 427: 13.692 distance: 421 - 428: 8.000 distance: 422 - 423: 10.482 distance: 422 - 424: 14.690 distance: 422 - 429: 6.620 distance: 423 - 430: 13.249 distance: 423 - 431: 19.549 distance: 423 - 432: 24.582 distance: 424 - 433: 8.282 distance: 424 - 434: 8.460 distance: 424 - 435: 9.703 distance: 436 - 437: 6.025 distance: 436 - 440: 11.869 distance: 437 - 438: 16.620 distance: 437 - 441: 24.583 distance: 437 - 442: 19.370 distance: 438 - 439: 8.876 distance: 438 - 443: 18.172 distance: 443 - 444: 20.064 distance: 443 - 447: 26.010 distance: 444 - 445: 12.358 distance: 444 - 448: 7.559 distance: 444 - 449: 26.053 distance: 445 - 446: 34.378 distance: 445 - 450: 51.150 distance: 450 - 451: 16.615 distance: 450 - 458: 11.463 distance: 451 - 452: 41.691 distance: 451 - 454: 27.595 distance: 451 - 459: 17.139 distance: 452 - 469: 26.344 distance: 454 - 455: 19.648 distance: 454 - 456: 27.901 distance: 454 - 460: 29.959 distance: 455 - 457: 21.884 distance: 455 - 461: 28.355 distance: 455 - 462: 21.930 distance: 456 - 463: 11.213 distance: 456 - 464: 8.965 distance: 456 - 465: 3.850 distance: 457 - 466: 8.716 distance: 457 - 467: 24.848 distance: 457 - 468: 20.645 distance: 469 - 470: 33.363 distance: 469 - 476: 10.941 distance: 470 - 471: 4.328 distance: 470 - 473: 23.611 distance: 470 - 477: 34.326 distance: 471 - 472: 17.264 distance: 471 - 483: 11.534 distance: 473 - 474: 9.997 distance: 473 - 475: 28.938 distance: 473 - 478: 19.671 distance: 474 - 479: 32.350 distance: 475 - 480: 9.522 distance: 475 - 481: 15.091 distance: 475 - 482: 31.149 distance: 483 - 484: 24.263 distance: 483 - 490: 12.077 distance: 484 - 485: 17.045 distance: 484 - 487: 13.545 distance: 484 - 491: 13.207 distance: 485 - 486: 14.704 distance: 485 - 499: 19.393 distance: 487 - 488: 14.127 distance: 487 - 489: 22.258 distance: 487 - 492: 13.584 distance: 488 - 493: 7.224 distance: 488 - 494: 7.758 distance: 488 - 495: 20.054 distance: 489 - 496: 6.685 distance: 489 - 497: 10.043 distance: 489 - 498: 21.153 distance: 499 - 500: 20.606 distance: 499 - 504: 18.595 distance: 500 - 501: 35.980 distance: 500 - 503: 29.645 distance: 500 - 505: 13.558 distance: 501 - 502: 17.806 distance: 501 - 509: 15.687 distance: 503 - 506: 6.840 distance: 503 - 507: 22.509 distance: 503 - 508: 16.687