Starting phenix.real_space_refine on Mon Sep 30 11:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/09_2024/7yi4_33851.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/09_2024/7yi4_33851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/09_2024/7yi4_33851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/09_2024/7yi4_33851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/09_2024/7yi4_33851.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/09_2024/7yi4_33851.cif" } resolution = 3.96 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 302 5.49 5 S 87 5.16 5 C 15143 2.51 5 N 4495 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25351 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2326 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2588 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 5 Chain: "F" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "P" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11022 SG CYS D 417 127.085 60.757 70.222 1.00548.42 S ATOM 11049 SG CYS D 420 128.395 57.216 70.769 1.00541.45 S ATOM 11305 SG CYS D 451 128.651 59.913 73.503 1.00488.09 S ATOM 9961 SG CYS D 263 92.512 95.032 76.495 1.00502.95 S ATOM 9978 SG CYS D 266 95.322 92.480 76.314 1.00506.17 S ATOM 10131 SG CYS D 286 96.001 95.688 78.071 1.00483.68 S ATOM 10266 SG CYS D 303 84.724 101.733 74.705 1.00517.62 S ATOM 10289 SG CYS D 306 80.870 104.261 73.937 1.00523.12 S ATOM 11210 SG CYS D 440 121.918 69.864 66.373 1.00572.63 S ATOM 11236 SG CYS D 443 124.633 69.527 63.545 1.00575.36 S ATOM 11425 SG CYS D 466 125.622 71.045 66.672 1.00567.07 S Time building chain proxies: 14.56, per 1000 atoms: 0.57 Number of scatterers: 25351 At special positions: 0 Unit cell: (177.53, 149.385, 145.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 87 16.00 P 302 15.00 O 5319 8.00 N 4495 7.00 C 15143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 420 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 263 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 306 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 440 " Number of angles added : 9 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 21 sheets defined 59.4% alpha, 7.7% beta 147 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 10.71 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.693A pdb=" N LEU A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.804A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 838 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 891 through 922 removed outlier: 3.784A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.865A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.081A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 4.110A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 3.728A pdb=" N VAL A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.954A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.501A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.240A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.077A pdb=" N GLY B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.758A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.527A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.321A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.505A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.935A pdb=" N ASN C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.637A pdb=" N ASP C 89 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 124 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.586A pdb=" N VAL C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 5.251A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 316 removed outlier: 4.377A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.985A pdb=" N SER C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.934A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 4.127A pdb=" N MET C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 168 through 175 removed outlier: 4.055A pdb=" N LEU D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.478A pdb=" N GLY D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 344 through 346 No H-bonds generated for 'chain 'D' and resid 344 through 346' Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.806A pdb=" N THR D 405 " --> pdb=" O ASN D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 544 through 564 removed outlier: 3.580A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 563 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.814A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 46 through 73 Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.516A pdb=" N LEU I 115 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 82 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 121 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 50 through 76 removed outlier: 3.708A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 46 through 73 Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 101 through 121 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.152A pdb=" N ASN E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 4.118A pdb=" N ASP E 89 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 124 Processing helix chain 'G' and resid 44 through 55 removed outlier: 3.587A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 75 Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.853A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 removed outlier: 3.594A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.974A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 64 removed outlier: 7.008A pdb=" N VAL B 21 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR B 64 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 142 " --> pdb=" O MET B 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 307 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.522A pdb=" N PHE C 78 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.759A pdb=" N LEU C 15 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA9, first strand: chain 'D' and resid 505 through 506 removed outlier: 3.818A pdb=" N TYR D 506 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 45 through 46 removed outlier: 7.527A pdb=" N ARG H 45 " --> pdb=" O ILE G 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 97 removed outlier: 6.416A pdb=" N THR H 96 " --> pdb=" O THR M 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.738A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 46 removed outlier: 7.939A pdb=" N ARG L 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AB9, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.185A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.677A pdb=" N GLN E 59 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 30 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS E 76 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.677A pdb=" N GLN E 59 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 25 " --> pdb=" O CYS E 14 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS E 14 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 15 " --> pdb=" O ARG E 98 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2997 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 18.48 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6819 1.34 - 1.46: 6865 1.46 - 1.58: 12052 1.58 - 1.70: 602 1.70 - 1.82: 137 Bond restraints: 26475 Sorted by residual: bond pdb=" CG MET B 47 " pdb=" SD MET B 47 " ideal model delta sigma weight residual 1.803 1.748 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CA MET B 305 " pdb=" CB MET B 305 " ideal model delta sigma weight residual 1.535 1.564 -0.029 2.09e-02 2.29e+03 1.88e+00 bond pdb=" N ALA M 47 " pdb=" CA ALA M 47 " ideal model delta sigma weight residual 1.463 1.454 0.009 6.90e-03 2.10e+04 1.62e+00 bond pdb=" CA LEU L 49 " pdb=" CB LEU L 49 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.34e-02 5.57e+03 1.40e+00 ... (remaining 26470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 36891 3.45 - 6.91: 99 6.91 - 10.36: 10 10.36 - 13.81: 7 13.81 - 17.27: 1 Bond angle restraints: 37008 Sorted by residual: angle pdb=" CA MET A1164 " pdb=" CB MET A1164 " pdb=" CG MET A1164 " ideal model delta sigma weight residual 114.10 125.18 -11.08 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA MET B 47 " pdb=" CB MET B 47 " pdb=" CG MET B 47 " ideal model delta sigma weight residual 114.10 124.46 -10.36 2.00e+00 2.50e-01 2.69e+01 angle pdb=" CA LEU L 49 " pdb=" CB LEU L 49 " pdb=" CG LEU L 49 " ideal model delta sigma weight residual 116.30 133.57 -17.27 3.50e+00 8.16e-02 2.43e+01 angle pdb=" N MET B 47 " pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 110.40 117.37 -6.97 1.63e+00 3.76e-01 1.83e+01 angle pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " pdb=" CD ARG E 110 " ideal model delta sigma weight residual 111.30 121.00 -9.70 2.30e+00 1.89e-01 1.78e+01 ... (remaining 37003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 13107 31.31 - 62.62: 1975 62.62 - 93.92: 73 93.92 - 125.23: 0 125.23 - 156.54: 1 Dihedral angle restraints: 15156 sinusoidal: 8247 harmonic: 6909 Sorted by residual: dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET B 61 " pdb=" C MET B 61 " pdb=" N GLU B 62 " pdb=" CA GLU B 62 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A1194 " pdb=" C MET A1194 " pdb=" N GLY A1195 " pdb=" CA GLY A1195 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 15153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2941 0.035 - 0.069: 879 0.069 - 0.104: 188 0.104 - 0.139: 59 0.139 - 0.173: 9 Chirality restraints: 4076 Sorted by residual: chirality pdb=" CA MET B 47 " pdb=" N MET B 47 " pdb=" C MET B 47 " pdb=" CB MET B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA GLU C 255 " pdb=" N GLU C 255 " pdb=" C GLU C 255 " pdb=" CB GLU C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA GLU A 918 " pdb=" N GLU A 918 " pdb=" C GLU A 918 " pdb=" CB GLU A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 4073 not shown) Planarity restraints: 3647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1164 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C MET A1164 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A1164 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A1165 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO D 119 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA O -35 " -0.027 2.00e-02 2.50e+03 1.20e-02 3.97e+00 pdb=" N9 DA O -35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA O -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA O -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA O -35 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA O -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA O -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA O -35 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA O -35 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA O -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA O -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 3644 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 340 2.61 - 3.18: 21588 3.18 - 3.76: 45805 3.76 - 4.33: 60120 4.33 - 4.90: 90715 Nonbonded interactions: 218568 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.041 2.230 nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.062 3.040 nonbonded pdb=" O2 DC O 70 " pdb=" N2 DG P -70 " model vdw 2.115 2.496 nonbonded pdb=" O2 DC O -21 " pdb=" N2 DG P 21 " model vdw 2.134 2.496 nonbonded pdb=" O2 DC O -50 " pdb=" N2 DG P 50 " model vdw 2.159 2.496 ... (remaining 218563 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 'G' and (resid 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 23 through 101) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 77.060 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.110 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:2.670 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.004 0.055 26475 Z= 0.199 Angle : 0.611 17.267 37008 Z= 0.345 Chirality : 0.036 0.173 4076 Planarity : 0.004 0.068 3647 Dihedral : 23.495 156.538 10692 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.10 % Allowed : 19.33 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2302 helix: 1.96 (0.15), residues: 1279 sheet: 0.32 (0.53), residues: 110 loop : -1.01 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 912 HIS 0.017 0.001 HIS B 43 PHE 0.014 0.001 PHE C 289 TYR 0.028 0.001 TYR L 88 ARG 0.011 0.000 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6705 (tpt) cc_final: 0.5145 (tmm) REVERT: B 61 MET cc_start: 0.7266 (mpp) cc_final: 0.6687 (mpp) REVERT: B 306 MET cc_start: 0.9071 (mmm) cc_final: 0.8567 (tpp) REVERT: D 316 MET cc_start: 0.7751 (mmm) cc_final: 0.7473 (mmm) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.3601 time to fit residues: 38.4789 Evaluate side-chains 61 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 50.0000 chunk 203 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 151 optimal weight: 0.9990 chunk 235 optimal weight: 40.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN C 101 ASN D 116 ASN N 44 GLN N 81 ASN E 80 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26475 Z= 0.174 Angle : 0.539 10.327 37008 Z= 0.307 Chirality : 0.036 0.150 4076 Planarity : 0.004 0.044 3647 Dihedral : 26.133 154.062 5889 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.15 % Allowed : 18.03 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2302 helix: 2.13 (0.14), residues: 1298 sheet: 0.30 (0.51), residues: 112 loop : -0.92 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 912 HIS 0.005 0.001 HIS B 49 PHE 0.012 0.001 PHE C 289 TYR 0.014 0.001 TYR E 38 ARG 0.005 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6725 (tpt) cc_final: 0.5078 (tmm) REVERT: A 773 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.6384 (pmm) REVERT: A 1194 MET cc_start: 0.4025 (ppp) cc_final: 0.3745 (ppp) REVERT: B 47 MET cc_start: 0.3106 (pmm) cc_final: 0.2642 (pmm) REVERT: B 61 MET cc_start: 0.7208 (mpp) cc_final: 0.6776 (mpp) REVERT: B 305 MET cc_start: 0.8418 (ppp) cc_final: 0.8100 (ppp) REVERT: B 315 MET cc_start: 0.2712 (pmm) cc_final: 0.1909 (pmm) REVERT: C 22 MET cc_start: 0.7898 (mpp) cc_final: 0.7426 (mmp) REVERT: C 256 MET cc_start: 0.9111 (ptp) cc_final: 0.8836 (ptp) REVERT: D 316 MET cc_start: 0.8083 (mmm) cc_final: 0.7796 (mmm) REVERT: H 92 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8904 (ptm160) REVERT: L 58 LEU cc_start: 0.9817 (OUTLIER) cc_final: 0.9552 (pp) REVERT: K 90 MET cc_start: 0.9177 (mmp) cc_final: 0.8847 (mmm) outliers start: 24 outliers final: 6 residues processed: 79 average time/residue: 0.3725 time to fit residues: 49.3737 Evaluate side-chains 70 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain E residue 22 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 254 optimal weight: 30.0000 chunk 209 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 HIS A 921 GLN D 503 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26475 Z= 0.216 Angle : 0.541 8.044 37008 Z= 0.306 Chirality : 0.036 0.190 4076 Planarity : 0.004 0.039 3647 Dihedral : 26.163 154.288 5889 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.73 % Allowed : 18.08 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2302 helix: 2.17 (0.14), residues: 1302 sheet: 0.39 (0.52), residues: 106 loop : -0.84 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 91 HIS 0.005 0.001 HIS B 43 PHE 0.010 0.001 PHE A 995 TYR 0.012 0.001 TYR E 38 ARG 0.005 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 60 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6749 (tpt) cc_final: 0.5415 (tmm) REVERT: A 773 MET cc_start: 0.7728 (ttt) cc_final: 0.6195 (pmm) REVERT: A 1194 MET cc_start: 0.4090 (ppp) cc_final: 0.3863 (ppp) REVERT: B 19 ARG cc_start: 0.3106 (OUTLIER) cc_final: 0.2594 (mtm180) REVERT: B 47 MET cc_start: 0.3134 (OUTLIER) cc_final: 0.2767 (pmm) REVERT: B 61 MET cc_start: 0.7283 (mpp) cc_final: 0.6923 (mpp) REVERT: B 305 MET cc_start: 0.8514 (ppp) cc_final: 0.8226 (ppp) REVERT: B 306 MET cc_start: 0.9001 (mmm) cc_final: 0.8740 (mmm) REVERT: B 315 MET cc_start: 0.2596 (pmm) cc_final: 0.1787 (pmm) REVERT: C 22 MET cc_start: 0.7639 (mpp) cc_final: 0.7351 (mmp) REVERT: C 256 MET cc_start: 0.9116 (ptp) cc_final: 0.8803 (ptp) REVERT: C 347 MET cc_start: 0.1775 (tpp) cc_final: 0.1568 (tpp) REVERT: D 316 MET cc_start: 0.8307 (mmm) cc_final: 0.8014 (mmm) REVERT: L 58 LEU cc_start: 0.9826 (OUTLIER) cc_final: 0.9581 (pp) outliers start: 36 outliers final: 15 residues processed: 91 average time/residue: 0.3501 time to fit residues: 53.0204 Evaluate side-chains 78 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain G residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.3232 > 50: distance: 36 - 53: 20.689 distance: 40 - 61: 22.477 distance: 44 - 66: 21.195 distance: 47 - 53: 21.625 distance: 48 - 71: 34.880 distance: 53 - 54: 8.271 distance: 54 - 55: 14.581 distance: 54 - 57: 7.024 distance: 55 - 56: 7.717 distance: 55 - 61: 6.151 distance: 56 - 78: 29.223 distance: 57 - 58: 32.463 distance: 58 - 59: 6.952 distance: 58 - 60: 7.841 distance: 62 - 63: 9.932 distance: 62 - 65: 12.676 distance: 63 - 64: 3.416 distance: 63 - 66: 4.201 distance: 64 - 86: 32.890 distance: 66 - 67: 5.769 distance: 67 - 68: 11.410 distance: 67 - 70: 12.178 distance: 68 - 69: 26.067 distance: 68 - 71: 44.893 distance: 69 - 95: 34.720 distance: 71 - 72: 39.672 distance: 72 - 73: 22.993 distance: 72 - 75: 30.195 distance: 73 - 74: 7.036 distance: 73 - 78: 12.138 distance: 74 - 107: 12.835 distance: 75 - 76: 20.954 distance: 75 - 77: 8.514 distance: 78 - 79: 23.067 distance: 79 - 80: 9.794 distance: 79 - 82: 25.035 distance: 80 - 81: 6.448 distance: 80 - 86: 14.416 distance: 81 - 115: 14.866 distance: 82 - 83: 6.715 distance: 83 - 84: 35.697 distance: 83 - 85: 14.518 distance: 86 - 87: 10.400 distance: 87 - 88: 12.981 distance: 87 - 90: 13.139 distance: 88 - 89: 8.092 distance: 88 - 95: 12.874 distance: 89 - 122: 15.497 distance: 90 - 91: 14.292 distance: 91 - 92: 18.051 distance: 92 - 93: 12.440 distance: 92 - 94: 13.782 distance: 95 - 96: 6.821 distance: 96 - 97: 16.109 distance: 96 - 99: 9.226 distance: 97 - 98: 17.999 distance: 97 - 107: 22.662 distance: 98 - 127: 26.093 distance: 99 - 100: 7.099 distance: 100 - 101: 4.698 distance: 100 - 102: 11.717 distance: 101 - 103: 6.146 distance: 102 - 104: 8.134 distance: 103 - 105: 7.571 distance: 104 - 105: 5.778 distance: 105 - 106: 7.998 distance: 107 - 108: 14.117 distance: 108 - 109: 7.607 distance: 108 - 111: 6.279 distance: 109 - 110: 6.559 distance: 109 - 115: 5.350 distance: 110 - 136: 24.217 distance: 111 - 112: 10.314 distance: 112 - 113: 19.078 distance: 112 - 114: 11.887 distance: 115 - 116: 13.331 distance: 116 - 117: 13.466 distance: 116 - 119: 11.048 distance: 117 - 118: 14.155 distance: 117 - 122: 9.027 distance: 118 - 141: 14.534 distance: 119 - 120: 16.054 distance: 119 - 121: 36.040 distance: 122 - 123: 10.766 distance: 123 - 124: 9.850 distance: 123 - 126: 11.731 distance: 124 - 125: 4.827 distance: 130 - 155: 3.036