Starting phenix.real_space_refine on Tue Nov 14 22:47:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/11_2023/8j3z_35968_updated.pdb" } resolution = 3.17 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= -0.001 sd= 0.029 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 P 6 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 6356 2.51 5 N 1647 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A GLU 1107": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1145": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A GLU 1169": "OE1" <-> "OE2" Residue "A GLU 1254": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9814 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9814 Unusual residues: {' MG': 2, 'ATP': 2, 'PUC': 1} Classifications: {'peptide': 1218, 'undetermined': 5} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178, None: 5} Not linked: pdbres="PRO A1298 " pdbres="ATP A1401 " Not linked: pdbres="ATP A1401 " pdbres=" MG A1402 " Not linked: pdbres=" MG A1402 " pdbres="PUC A1403 " Not linked: pdbres="PUC A1403 " pdbres=" MG A1404 " Not linked: pdbres=" MG A1404 " pdbres="ATP A1405 " Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Time building chain proxies: 5.60, per 1000 atoms: 0.57 Number of scatterers: 9814 At special positions: 0 Unit cell: (77.08, 92.66, 144.32, 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) S 43 16.00 P 6 15.00 Mg 2 11.99 O 1760 8.00 N 1647 7.00 C 6356 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 5 sheets defined 59.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 12 through 15 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 25 through 36 Proline residue: A 29 - end of helix removed outlier: 3.934A pdb=" N HIS A 35 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 36 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.660A pdb=" N PHE A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 146 Processing helix chain 'A' and resid 153 through 178 removed outlier: 3.996A pdb=" N GLN A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 191 through 200 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 213 through 250 removed outlier: 3.964A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 5.291A pdb=" N TRP A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY A 234 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 236 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 246 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 257 through 289 removed outlier: 3.737A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 318 through 325 removed outlier: 3.674A pdb=" N SER A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 350 through 366 removed outlier: 3.590A pdb=" N ALA A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 4.380A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 537 through 551 removed outlier: 3.748A pdb=" N GLN A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 594 through 599 removed outlier: 4.360A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 711 through 743 removed outlier: 3.741A pdb=" N VAL A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 794 removed outlier: 3.508A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 807 removed outlier: 4.141A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 818 through 834 removed outlier: 4.404A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 Processing helix chain 'A' and resid 862 through 909 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 4.250A pdb=" N ILE A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 879 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG A 880 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 881 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 882 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER A 886 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 889 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS A 890 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 898 " --> pdb=" O THR A 895 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 920 through 965 removed outlier: 3.671A pdb=" N VAL A 950 " --> pdb=" O ARG A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 976 through 989 removed outlier: 3.714A pdb=" N GLY A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1000 through 1006 removed outlier: 4.013A pdb=" N ASN A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1017 removed outlier: 3.779A pdb=" N ARG A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.785A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1110 through 1116 removed outlier: 4.076A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1136 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1182 through 1193 removed outlier: 3.587A pdb=" N LEU A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1209 through 1222 removed outlier: 5.166A pdb=" N GLN A1216 " --> pdb=" O ASP A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.875A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1296 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 436 Processing sheet with id= B, first strand: chain 'A' and resid 611 through 615 removed outlier: 6.992A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLY A 445 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= D, first strand: chain 'A' and resid 1251 through 1256 removed outlier: 6.779A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASP A1201 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A1120 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 415 through 417 removed outlier: 7.511A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1218 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: 3.55 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1671 1.32 - 1.45: 2568 1.45 - 1.57: 5707 1.57 - 1.69: 10 1.69 - 1.81: 70 Bond restraints: 10026 Sorted by residual: bond pdb=" C12 PUC A1403 " pdb=" C13 PUC A1403 " ideal model delta sigma weight residual 1.704 1.500 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C7 PUC A1403 " pdb=" C8 PUC A1403 " ideal model delta sigma weight residual 1.707 1.522 0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C21 PUC A1403 " pdb=" C9 PUC A1403 " ideal model delta sigma weight residual 1.347 1.517 -0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" C4 ATP A1401 " pdb=" C5 ATP A1401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C10 PUC A1403 " pdb=" C9 PUC A1403 " ideal model delta sigma weight residual 1.675 1.523 0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 10021 not shown) Histogram of bond angle deviations from ideal: 92.06 - 100.85: 16 100.85 - 109.64: 1218 109.64 - 118.43: 6727 118.43 - 127.23: 5527 127.23 - 136.02: 109 Bond angle restraints: 13597 Sorted by residual: angle pdb=" PB ATP A1401 " pdb=" O3B ATP A1401 " pdb=" PG ATP A1401 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PA ATP A1401 " pdb=" O3A ATP A1401 " pdb=" PB ATP A1401 " ideal model delta sigma weight residual 136.83 122.82 14.01 1.00e+00 1.00e+00 1.96e+02 angle pdb=" C5 PUC A1403 " pdb=" C6 PUC A1403 " pdb=" C7 PUC A1403 " ideal model delta sigma weight residual 152.66 126.75 25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" N LEU A 93 " pdb=" CA LEU A 93 " pdb=" C LEU A 93 " ideal model delta sigma weight residual 113.43 103.13 10.30 1.26e+00 6.30e-01 6.69e+01 angle pdb=" C5 ATP A1401 " pdb=" C4 ATP A1401 " pdb=" N3 ATP A1401 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.68e+01 ... (remaining 13592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5359 17.65 - 35.30: 510 35.30 - 52.96: 79 52.96 - 70.61: 10 70.61 - 88.26: 5 Dihedral angle restraints: 5963 sinusoidal: 2405 harmonic: 3558 Sorted by residual: dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N ILE A 85 " pdb=" CA ILE A 85 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU A 316 " pdb=" C LEU A 316 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG A 946 " pdb=" C ARG A 946 " pdb=" N TRP A 947 " pdb=" CA TRP A 947 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 1573 1.044 - 2.087: 0 2.087 - 3.131: 0 3.131 - 4.174: 0 4.174 - 5.217: 1 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C12 PUC A1403 " pdb=" C11 PUC A1403 " pdb=" C13 PUC A1403 " pdb=" C8 PUC A1403 " both_signs ideal model delta sigma weight residual False -2.55 2.67 -5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" CA TRP A 89 " pdb=" N TRP A 89 " pdb=" C TRP A 89 " pdb=" CB TRP A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C9 PUC A1403 " pdb=" C10 PUC A1403 " pdb=" C21 PUC A1403 " pdb=" C8 PUC A1403 " both_signs ideal model delta sigma weight residual False 2.91 3.17 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1571 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 PUC A1403 " 0.064 2.00e-02 2.50e+03 2.53e-01 6.42e+02 pdb=" C5 PUC A1403 " 0.135 2.00e-02 2.50e+03 pdb=" C6 PUC A1403 " -0.427 2.00e-02 2.50e+03 pdb=" C7 PUC A1403 " 0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 PUC A1403 " -0.220 2.00e-02 2.50e+03 2.08e-01 4.34e+02 pdb=" C13 PUC A1403 " 0.272 2.00e-02 2.50e+03 pdb=" C14 PUC A1403 " 0.133 2.00e-02 2.50e+03 pdb=" C15 PUC A1403 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1016 " 0.024 2.00e-02 2.50e+03 2.05e-02 8.37e+00 pdb=" CG TYR A1016 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A1016 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A1016 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1016 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1016 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A1016 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1016 " -0.000 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 108 2.56 - 3.15: 8515 3.15 - 3.73: 15707 3.73 - 4.32: 23057 4.32 - 4.90: 37225 Nonbonded interactions: 84612 Sorted by model distance: nonbonded pdb=" O2B ATP A1401 " pdb="MG MG A1402 " model vdw 1.975 2.170 nonbonded pdb=" O3G ATP A1401 " pdb="MG MG A1402 " model vdw 2.057 2.170 nonbonded pdb=" O LEU A 717 " pdb=" ND2 ASN A 721 " model vdw 2.194 2.520 nonbonded pdb=" OG SER A 794 " pdb=" OD1 ASP A 833 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASN A1047 " pdb=" N HIS A1060 " model vdw 2.200 2.520 ... (remaining 84607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.130 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.790 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.009 0.204 10026 Z= 0.617 Angle : 0.952 25.907 13597 Z= 0.558 Chirality : 0.141 5.217 1574 Planarity : 0.009 0.253 1677 Dihedral : 13.757 88.260 3657 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.28 % Allowed : 1.04 % Favored : 98.68 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.56 % 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: -1.65 (0.23), residues: 1212 helix: -1.09 (0.18), residues: 767 sheet: -0.20 (0.65), residues: 62 loop : -0.84 (0.32), residues: 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.067 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.2174 time to fit residues: 46.0040 Evaluate side-chains 126 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1104 time to fit residues: 1.7558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 95 optimal weight: 0.0060 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 HIS A 710 HIS ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10026 Z= 0.167 Angle : 0.623 12.172 13597 Z= 0.318 Chirality : 0.045 0.655 1574 Planarity : 0.004 0.050 1677 Dihedral : 6.350 79.480 1336 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.47 % Allowed : 7.91 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.23), residues: 1212 helix: -0.83 (0.18), residues: 780 sheet: -0.13 (0.65), residues: 62 loop : -0.78 (0.31), residues: 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.066 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 149 average time/residue: 0.2431 time to fit residues: 50.5281 Evaluate side-chains 135 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0977 time to fit residues: 2.1065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10026 Z= 0.196 Angle : 0.598 10.596 13597 Z= 0.304 Chirality : 0.042 0.429 1574 Planarity : 0.004 0.051 1677 Dihedral : 6.526 76.905 1336 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.13 % Allowed : 10.92 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.09 (0.24), residues: 1212 helix: -0.69 (0.18), residues: 781 sheet: 0.07 (0.65), residues: 62 loop : -0.54 (0.32), residues: 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 0.2336 time to fit residues: 48.5075 Evaluate side-chains 140 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1042 time to fit residues: 3.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN A 699 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10026 Z= 0.361 Angle : 0.652 9.714 13597 Z= 0.330 Chirality : 0.044 0.298 1574 Planarity : 0.004 0.046 1677 Dihedral : 6.431 70.111 1336 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.04 % Allowed : 13.09 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.16 (0.24), residues: 1212 helix: -0.75 (0.18), residues: 774 sheet: 0.16 (0.65), residues: 62 loop : -0.55 (0.33), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.072 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 149 average time/residue: 0.2497 time to fit residues: 52.8748 Evaluate side-chains 143 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1143 time to fit residues: 2.3079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN A 699 GLN A 710 HIS ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10026 Z= 0.173 Angle : 0.567 11.060 13597 Z= 0.291 Chirality : 0.041 0.166 1574 Planarity : 0.004 0.049 1677 Dihedral : 6.241 69.320 1336 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.94 % Allowed : 14.12 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1212 helix: -0.50 (0.18), residues: 771 sheet: 0.17 (0.58), residues: 74 loop : -0.50 (0.33), residues: 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 152 average time/residue: 0.2294 time to fit residues: 49.9759 Evaluate side-chains 140 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1041 time to fit residues: 2.3346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 97 optimal weight: 0.0010 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN A 849 GLN ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10026 Z= 0.192 Angle : 0.560 10.809 13597 Z= 0.285 Chirality : 0.041 0.169 1574 Planarity : 0.004 0.048 1677 Dihedral : 6.034 66.374 1336 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.75 % Allowed : 14.97 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1212 helix: -0.36 (0.19), residues: 771 sheet: 0.42 (0.66), residues: 62 loop : -0.40 (0.33), residues: 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 0.2193 time to fit residues: 44.9991 Evaluate side-chains 138 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0956 time to fit residues: 2.3584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10026 Z= 0.176 Angle : 0.562 15.245 13597 Z= 0.284 Chirality : 0.041 0.162 1574 Planarity : 0.004 0.049 1677 Dihedral : 5.863 63.979 1336 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.56 % Allowed : 15.91 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1212 helix: -0.21 (0.19), residues: 776 sheet: 0.43 (0.66), residues: 62 loop : -0.32 (0.33), residues: 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 146 average time/residue: 0.2323 time to fit residues: 48.4885 Evaluate side-chains 139 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1046 time to fit residues: 2.1274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 51.6543 > 50: distance: 103 - 104: 4.980 distance: 104 - 105: 8.104 distance: 104 - 107: 5.304 distance: 105 - 106: 11.792 distance: 105 - 109: 6.479 distance: 106 - 130: 8.017 distance: 107 - 108: 4.688 distance: 109 - 110: 4.808 distance: 110 - 113: 6.724 distance: 111 - 112: 16.913 distance: 114 - 115: 3.861 distance: 115 - 116: 11.933 distance: 115 - 118: 9.149 distance: 116 - 117: 4.782 distance: 116 - 123: 11.032 distance: 117 - 147: 10.363 distance: 118 - 119: 4.571 distance: 119 - 120: 10.829 distance: 120 - 121: 6.247 distance: 120 - 122: 10.448 distance: 123 - 124: 8.905 distance: 124 - 125: 11.856 distance: 124 - 127: 5.338 distance: 125 - 126: 11.416 distance: 125 - 130: 11.768 distance: 127 - 128: 8.129 distance: 127 - 129: 5.406 distance: 131 - 132: 4.291 distance: 131 - 134: 4.823 distance: 132 - 133: 11.516 distance: 132 - 139: 5.967 distance: 134 - 135: 10.790 distance: 135 - 136: 7.238 distance: 136 - 137: 3.169 distance: 136 - 138: 8.384 distance: 139 - 140: 4.176 distance: 140 - 141: 8.538 distance: 140 - 143: 7.752 distance: 141 - 147: 6.921 distance: 143 - 144: 5.158 distance: 144 - 145: 5.191 distance: 144 - 146: 3.564 distance: 148 - 151: 8.001 distance: 149 - 150: 5.455 distance: 149 - 155: 6.525 distance: 151 - 152: 8.939 distance: 152 - 153: 19.072 distance: 153 - 154: 26.558 distance: 155 - 156: 5.151 distance: 156 - 159: 4.663 distance: 157 - 158: 3.561 distance: 157 - 163: 10.879 distance: 159 - 160: 5.768 distance: 160 - 161: 13.791 distance: 161 - 162: 3.008 distance: 163 - 164: 6.627 distance: 164 - 165: 11.111 distance: 164 - 167: 3.642 distance: 165 - 166: 30.684 distance: 165 - 171: 14.314 distance: 167 - 168: 12.720 distance: 167 - 169: 5.812 distance: 168 - 170: 13.168 distance: 171 - 172: 7.885 distance: 172 - 173: 11.478 distance: 172 - 175: 16.264 distance: 173 - 174: 22.759 distance: 173 - 177: 10.237 distance: 175 - 176: 7.500