Starting phenix.real_space_refine on Thu Mar 14 21:32:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_35968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_35968.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_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_35968/03_2024/8j3z_35968_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_35968_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_35968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_35968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_35968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3z_35968/03_2024/8j3z_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-dev-5265/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: 5.37, per 1000 atoms: 0.55 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 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: 2.95 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: 3.59 Time building geometry restraints manager: 4.21 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 - 17.99: 5409 17.99 - 35.98: 509 35.98 - 53.97: 88 53.97 - 71.96: 12 71.96 - 89.95: 7 Dihedral angle restraints: 6025 sinusoidal: 2467 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 6022 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: 0.890 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: 6.050 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 30.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- 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 : 14.285 89.946 3719 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 89 HIS 0.007 0.001 HIS A 710 PHE 0.023 0.002 PHE A 352 TYR 0.050 0.003 TYR A1016 ARG 0.009 0.001 ARG A 362 *********************** 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 : 1.073 Fit side-chains REVERT: A 783 SER cc_start: 0.8485 (m) cc_final: 0.8249 (m) REVERT: A 1216 GLN cc_start: 0.7235 (mp10) cc_final: 0.6838 (mp10) outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.2115 time to fit residues: 44.7578 Evaluate side-chains 127 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU 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: 0.7980 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: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0954 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= 0.183 Angle : 0.629 11.894 13597 Z= 0.321 Chirality : 0.046 0.742 1574 Planarity : 0.004 0.051 1677 Dihedral : 8.170 69.473 1402 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.47 % Allowed : 7.53 % Favored : 92.00 % 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: -1.37 (0.23), residues: 1212 helix: -0.84 (0.18), residues: 780 sheet: -0.13 (0.65), residues: 62 loop : -0.78 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.006 0.001 HIS A 934 PHE 0.024 0.001 PHE A 336 TYR 0.031 0.001 TYR A1016 ARG 0.004 0.000 ARG A 474 *********************** 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 150 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 1.161 Fit side-chains REVERT: A 276 MET cc_start: 0.8036 (tpt) cc_final: 0.7596 (tpt) REVERT: A 433 PHE cc_start: 0.7879 (p90) cc_final: 0.7649 (p90) REVERT: A 783 SER cc_start: 0.8377 (m) cc_final: 0.8156 (m) REVERT: A 1131 MET cc_start: 0.4883 (mmp) cc_final: 0.4604 (mmp) REVERT: A 1216 GLN cc_start: 0.7062 (mp10) cc_final: 0.6693 (mp10) outliers start: 5 outliers final: 1 residues processed: 147 average time/residue: 0.2363 time to fit residues: 48.5855 Evaluate side-chains 132 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 89 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10026 Z= 0.230 Angle : 0.610 11.712 13597 Z= 0.310 Chirality : 0.043 0.509 1574 Planarity : 0.004 0.048 1677 Dihedral : 7.988 64.037 1398 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.41 % Allowed : 10.45 % Favored : 88.14 % 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: -1.21 (0.24), residues: 1212 helix: -0.75 (0.18), residues: 779 sheet: 0.02 (0.65), residues: 62 loop : -0.66 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 89 HIS 0.005 0.001 HIS A 934 PHE 0.023 0.001 PHE A 336 TYR 0.021 0.001 TYR A1016 ARG 0.004 0.000 ARG A 474 *********************** 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: 15 poor density : 139 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 783 SER cc_start: 0.8423 (m) cc_final: 0.8193 (m) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 0.2277 time to fit residues: 45.8755 Evaluate side-chains 139 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1170 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7714 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10026 Z= 0.247 Angle : 0.601 10.191 13597 Z= 0.306 Chirality : 0.043 0.348 1574 Planarity : 0.004 0.048 1677 Dihedral : 7.996 61.062 1398 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.79 % Allowed : 12.34 % 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: -1.10 (0.24), residues: 1212 helix: -0.69 (0.18), residues: 779 sheet: 0.15 (0.65), residues: 62 loop : -0.56 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 89 HIS 0.005 0.001 HIS A 934 PHE 0.023 0.001 PHE A 336 TYR 0.019 0.001 TYR A1016 ARG 0.004 0.000 ARG A 474 *********************** 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 164 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 276 MET cc_start: 0.7985 (tpt) cc_final: 0.7635 (tpt) REVERT: A 607 LYS cc_start: 0.7357 (tttp) cc_final: 0.6939 (tttm) REVERT: A 783 SER cc_start: 0.8413 (m) cc_final: 0.8185 (m) REVERT: A 1008 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 1217 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7979 (mtmm) outliers start: 19 outliers final: 10 residues processed: 154 average time/residue: 0.2310 time to fit residues: 50.8138 Evaluate side-chains 149 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 0 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7670 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10026 Z= 0.177 Angle : 0.555 10.956 13597 Z= 0.284 Chirality : 0.041 0.178 1574 Planarity : 0.004 0.053 1677 Dihedral : 7.676 64.325 1398 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.69 % Allowed : 12.81 % Favored : 85.50 % 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: -0.89 (0.24), residues: 1212 helix: -0.52 (0.18), residues: 777 sheet: 0.23 (0.59), residues: 74 loop : -0.52 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.005 0.001 HIS A 934 PHE 0.024 0.001 PHE A 336 TYR 0.015 0.001 TYR A1016 ARG 0.006 0.000 ARG A 503 *********************** 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 165 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 474 ARG cc_start: 0.6724 (mtm110) cc_final: 0.5810 (ptt-90) REVERT: A 607 LYS cc_start: 0.7330 (tttp) cc_final: 0.6907 (tttm) REVERT: A 783 SER cc_start: 0.8372 (m) cc_final: 0.8142 (m) REVERT: A 1008 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 1213 GLU cc_start: 0.6471 (pp20) cc_final: 0.6210 (mp0) outliers start: 18 outliers final: 13 residues processed: 155 average time/residue: 0.2178 time to fit residues: 48.3497 Evaluate side-chains 154 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10026 Z= 0.402 Angle : 0.664 10.766 13597 Z= 0.335 Chirality : 0.045 0.196 1574 Planarity : 0.005 0.059 1677 Dihedral : 7.909 64.672 1398 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.98 % Allowed : 14.03 % Favored : 83.99 % 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: -1.06 (0.24), residues: 1212 helix: -0.72 (0.18), residues: 773 sheet: 0.38 (0.66), residues: 62 loop : -0.46 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 947 HIS 0.007 0.001 HIS A 213 PHE 0.022 0.002 PHE A 336 TYR 0.022 0.002 TYR A 504 ARG 0.007 0.001 ARG A 503 *********************** 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 162 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 243 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 276 MET cc_start: 0.8077 (tpt) cc_final: 0.7205 (tpt) REVERT: A 607 LYS cc_start: 0.7365 (tttp) cc_final: 0.6940 (tttm) REVERT: A 805 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7015 (tt) REVERT: A 1008 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 1213 GLU cc_start: 0.6495 (pp20) cc_final: 0.6101 (mp0) outliers start: 21 outliers final: 16 residues processed: 150 average time/residue: 0.2222 time to fit residues: 47.2022 Evaluate side-chains 154 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1117 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS A 849 GLN ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10026 Z= 0.184 Angle : 0.575 11.378 13597 Z= 0.294 Chirality : 0.041 0.154 1574 Planarity : 0.004 0.061 1677 Dihedral : 7.602 68.637 1398 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.60 % Allowed : 15.54 % Favored : 82.86 % 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: -0.72 (0.24), residues: 1212 helix: -0.43 (0.19), residues: 772 sheet: 0.27 (0.59), residues: 74 loop : -0.35 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.005 0.001 HIS A 934 PHE 0.026 0.001 PHE A 336 TYR 0.013 0.001 TYR A1016 ARG 0.008 0.000 ARG A 503 *********************** 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 156 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 243 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 474 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6085 (ptt-90) REVERT: A 607 LYS cc_start: 0.7291 (tttp) cc_final: 0.6865 (tttm) REVERT: A 1008 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 1213 GLU cc_start: 0.6472 (pp20) cc_final: 0.6264 (mp0) outliers start: 17 outliers final: 8 residues processed: 151 average time/residue: 0.2126 time to fit residues: 45.7485 Evaluate side-chains 143 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1008 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 580 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1990 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= 0.184 Angle : 0.575 15.796 13597 Z= 0.291 Chirality : 0.041 0.159 1574 Planarity : 0.004 0.065 1677 Dihedral : 7.406 69.928 1398 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.13 % Allowed : 16.29 % Favored : 82.58 % 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: -0.51 (0.24), residues: 1212 helix: -0.28 (0.19), residues: 769 sheet: 0.35 (0.60), residues: 74 loop : -0.22 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.004 0.001 HIS A 934 PHE 0.023 0.001 PHE A 901 TYR 0.022 0.001 TYR A 504 ARG 0.009 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 8 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 152 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 243 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8710 (p) REVERT: A 409 MET cc_start: 0.7049 (ptt) cc_final: 0.6832 (ptm) REVERT: A 551 GLN cc_start: 0.7174 (tp40) cc_final: 0.6962 (mm110) REVERT: A 607 LYS cc_start: 0.7267 (tttp) cc_final: 0.6839 (tttm) REVERT: A 1008 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7822 (tt) outliers start: 12 outliers final: 8 residues processed: 147 average time/residue: 0.2259 time to fit residues: 46.9003 Evaluate side-chains 145 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1008 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10026 Z= 0.217 Angle : 0.589 15.465 13597 Z= 0.296 Chirality : 0.042 0.156 1574 Planarity : 0.004 0.069 1677 Dihedral : 7.364 69.601 1398 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.13 % Allowed : 17.14 % Favored : 81.73 % 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: -0.50 (0.24), residues: 1212 helix: -0.28 (0.19), residues: 776 sheet: 0.37 (0.60), residues: 74 loop : -0.19 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.004 0.001 HIS A 934 PHE 0.022 0.001 PHE A 336 TYR 0.013 0.001 TYR A1016 ARG 0.008 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 9 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: 12 poor density : 135 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 243 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 409 MET cc_start: 0.7033 (ptt) cc_final: 0.6794 (ptm) REVERT: A 474 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6208 (ptt-90) REVERT: A 607 LYS cc_start: 0.7248 (tttp) cc_final: 0.6818 (tttm) REVERT: A 1008 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (tt) outliers start: 12 outliers final: 9 residues processed: 142 average time/residue: 0.2373 time to fit residues: 47.4950 Evaluate side-chains 144 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN ** A 580 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: 0.7633 moved from start: 0.2241 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= 0.169 Angle : 0.566 15.390 13597 Z= 0.284 Chirality : 0.041 0.145 1574 Planarity : 0.004 0.069 1677 Dihedral : 7.192 71.571 1398 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.32 % Allowed : 16.76 % Favored : 81.92 % 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: -0.36 (0.24), residues: 1212 helix: -0.15 (0.19), residues: 778 sheet: 0.45 (0.61), residues: 74 loop : -0.19 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.004 0.001 HIS A 934 PHE 0.023 0.001 PHE A 336 TYR 0.021 0.001 TYR A 504 ARG 0.008 0.000 ARG A 503 ********************** REFINEMENT MACRO_CYCLE 10 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: 14 poor density : 140 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 243 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8700 (p) REVERT: A 409 MET cc_start: 0.7082 (ptt) cc_final: 0.6819 (ptm) REVERT: A 474 ARG cc_start: 0.7100 (mtm110) cc_final: 0.6301 (ptt-90) REVERT: A 607 LYS cc_start: 0.7223 (tttp) cc_final: 0.6790 (tttm) REVERT: A 805 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6979 (tt) REVERT: A 1007 MET cc_start: 0.7924 (tpp) cc_final: 0.7616 (tpt) REVERT: A 1008 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7760 (tt) outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.2389 time to fit residues: 50.8086 Evaluate side-chains 146 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1117 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.207133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147081 restraints weight = 11224.441| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.15 r_work: 0.3667 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2238 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= 0.207 Angle : 0.579 15.055 13597 Z= 0.290 Chirality : 0.041 0.153 1574 Planarity : 0.004 0.070 1677 Dihedral : 7.161 70.670 1398 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.22 % Allowed : 16.85 % Favored : 81.92 % 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: -0.39 (0.24), residues: 1212 helix: -0.19 (0.18), residues: 788 sheet: 0.47 (0.57), residues: 84 loop : -0.20 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.005 0.001 HIS A 934 PHE 0.022 0.001 PHE A 336 TYR 0.012 0.001 TYR A1016 ARG 0.008 0.000 ARG A 503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.20 seconds wall clock time: 43 minutes 36.03 seconds (2616.03 seconds total)