Starting phenix.real_space_refine (version: dev) on Mon Feb 20 18:27:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/02_2023/7vh3_31985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/02_2023/7vh3_31985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/02_2023/7vh3_31985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/02_2023/7vh3_31985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/02_2023/7vh3_31985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/02_2023/7vh3_31985.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1591": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1741": "NH1" <-> "NH2" Residue "A ARG 1796": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12749 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1612, 12749 Classifications: {'peptide': 1612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 46, 'TRANS': 1565} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Time building chain proxies: 7.12, per 1000 atoms: 0.56 Number of scatterers: 12749 At special positions: 0 Unit cell: (113.98, 109.06, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2389 8.00 N 2129 7.00 C 8144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1650 " - pdb=" SG CYS A1664 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.04 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: 4.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 48.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.722A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.888A pdb=" N ALA A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.650A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.268A pdb=" N SER A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 Processing helix chain 'A' and resid 108 through 125 removed outlier: 4.100A pdb=" N GLU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 164 through 175 removed outlier: 4.294A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.535A pdb=" N ASN A 203 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.589A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.799A pdb=" N LEU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.909A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.907A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 5.573A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.849A pdb=" N ARG A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 479 through 499 removed outlier: 3.662A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.790A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 598 Processing helix chain 'A' and resid 602 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 626 through 644 removed outlier: 4.011A pdb=" N ARG A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 637 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.946A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.953A pdb=" N VAL A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 713 through 732 removed outlier: 3.630A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 788 Processing helix chain 'A' and resid 835 through 852 removed outlier: 4.437A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 Processing helix chain 'A' and resid 887 through 895 removed outlier: 4.530A pdb=" N MET A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 918 Processing helix chain 'A' and resid 961 through 969 removed outlier: 3.730A pdb=" N ASP A 969 " --> pdb=" O HIS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1024 through 1033 Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 4.148A pdb=" N LEU A1091 " --> pdb=" O ASN A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1156 removed outlier: 3.866A pdb=" N VAL A1145 " --> pdb=" O MET A1141 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1181 removed outlier: 3.587A pdb=" N PHE A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 3.996A pdb=" N MET A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 removed outlier: 3.659A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 removed outlier: 4.577A pdb=" N ILE A1227 " --> pdb=" O SER A1223 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A1230 " --> pdb=" O SER A1226 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1273 Processing helix chain 'A' and resid 1295 through 1318 removed outlier: 3.611A pdb=" N TYR A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 3.584A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 4.204A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1428 removed outlier: 3.592A pdb=" N ASP A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1450 removed outlier: 3.568A pdb=" N SER A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1483 Processing helix chain 'A' and resid 1491 through 1506 removed outlier: 3.534A pdb=" N ASP A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1520 removed outlier: 3.879A pdb=" N ILE A1519 " --> pdb=" O LEU A1515 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1515 through 1520' Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.970A pdb=" N VAL A1541 " --> pdb=" O SER A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 Processing helix chain 'A' and resid 1614 through 1624 removed outlier: 3.650A pdb=" N GLY A1620 " --> pdb=" O SER A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1646 removed outlier: 3.539A pdb=" N VAL A1643 " --> pdb=" O TYR A1639 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A1646 " --> pdb=" O GLU A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1692 Processing helix chain 'A' and resid 1743 through 1750 removed outlier: 3.590A pdb=" N GLU A1750 " --> pdb=" O VAL A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.735A pdb=" N MET A1781 " --> pdb=" O ILE A1777 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1777 through 1782' Processing helix chain 'A' and resid 1788 through 1792 removed outlier: 3.886A pdb=" N HIS A1791 " --> pdb=" O ILE A1788 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.517A pdb=" N THR A 94 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.849A pdb=" N PHE A 533 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 559 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 566 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 459 removed outlier: 3.557A pdb=" N VAL A 523 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA6, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.729A pdb=" N GLU A1237 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1183 through 1184 removed outlier: 3.518A pdb=" N LEU A1183 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A1332 " --> pdb=" O TYR A1325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AB1, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AB2, first strand: chain 'A' and resid 1716 through 1718 481 hydrogen bonds defined for protein. 1395 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: 4.12 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3714 1.34 - 1.46: 2395 1.46 - 1.58: 6731 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 12967 Sorted by residual: bond pdb=" CA LEU A1288 " pdb=" CB LEU A1288 " ideal model delta sigma weight residual 1.525 1.554 -0.030 1.25e-02 6.40e+03 5.72e+00 bond pdb=" C LEU A 580 " pdb=" N PRO A 581 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.41e+00 bond pdb=" CB ASN A 344 " pdb=" CG ASN A 344 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.37e+00 bond pdb=" CA SER A 950 " pdb=" C SER A 950 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.50e+00 bond pdb=" CB PHE A1386 " pdb=" CG PHE A1386 " ideal model delta sigma weight residual 1.502 1.538 -0.036 2.30e-02 1.89e+03 2.48e+00 ... (remaining 12962 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.62: 161 104.62 - 111.98: 5875 111.98 - 119.34: 4842 119.34 - 126.71: 6468 126.71 - 134.07: 141 Bond angle restraints: 17487 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 109.34 126.31 -16.97 2.08e+00 2.31e-01 6.65e+01 angle pdb=" N LEU A 388 " pdb=" CA LEU A 388 " pdb=" C LEU A 388 " ideal model delta sigma weight residual 108.19 117.45 -9.26 1.29e+00 6.01e-01 5.15e+01 angle pdb=" N VAL A 389 " pdb=" CA VAL A 389 " pdb=" C VAL A 389 " ideal model delta sigma weight residual 109.34 122.95 -13.61 2.08e+00 2.31e-01 4.28e+01 angle pdb=" C LEU A 260 " pdb=" N THR A 261 " pdb=" CA THR A 261 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C LEU A1365 " pdb=" N ASN A1366 " pdb=" CA ASN A1366 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 ... (remaining 17482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 7286 15.42 - 30.84: 482 30.84 - 46.26: 119 46.26 - 61.68: 10 61.68 - 77.11: 7 Dihedral angle restraints: 7904 sinusoidal: 3187 harmonic: 4717 Sorted by residual: dihedral pdb=" CA LEU A 702 " pdb=" C LEU A 702 " pdb=" N CYS A 703 " pdb=" CA CYS A 703 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLY A1694 " pdb=" C GLY A1694 " pdb=" N GLU A1695 " pdb=" CA GLU A1695 " ideal model delta harmonic sigma weight residual -180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA THR A 710 " pdb=" C THR A 710 " pdb=" N PRO A 711 " pdb=" CA PRO A 711 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1639 0.070 - 0.140: 323 0.140 - 0.210: 37 0.210 - 0.280: 12 0.280 - 0.350: 4 Chirality restraints: 2015 Sorted by residual: chirality pdb=" CA ILE A 396 " pdb=" N ILE A 396 " pdb=" C ILE A 396 " pdb=" CB ILE A 396 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB ILE A1510 " pdb=" CA ILE A1510 " pdb=" CG1 ILE A1510 " pdb=" CG2 ILE A1510 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA VAL A 389 " pdb=" N VAL A 389 " pdb=" C VAL A 389 " pdb=" CB VAL A 389 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2012 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1290 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C MET A1290 " 0.052 2.00e-02 2.50e+03 pdb=" O MET A1290 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A1291 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 950 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO A 951 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 951 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 951 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 261 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C THR A 261 " -0.041 2.00e-02 2.50e+03 pdb=" O THR A 261 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 262 " 0.014 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2918 2.79 - 3.31: 11783 3.31 - 3.84: 20916 3.84 - 4.37: 24168 4.37 - 4.90: 40430 Nonbonded interactions: 100215 Sorted by model distance: nonbonded pdb=" OG SER A1098 " pdb=" OG SER A1101 " model vdw 2.257 2.440 nonbonded pdb=" O VAL A 770 " pdb=" OG SER A1363 " model vdw 2.304 2.440 nonbonded pdb=" CG2 VAL A1001 " pdb=" N LEU A1002 " model vdw 2.314 3.540 nonbonded pdb=" O GLU A1695 " pdb=" OG SER A1816 " model vdw 2.324 2.440 nonbonded pdb=" OG SER A 121 " pdb=" OH TYR A 835 " model vdw 2.331 2.440 ... (remaining 100210 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8144 2.51 5 N 2129 2.21 5 O 2389 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 3.990 Check model and map are aligned: 0.190 Process input model: 32.700 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 12967 Z= 0.334 Angle : 1.095 16.966 17487 Z= 0.579 Chirality : 0.059 0.350 2015 Planarity : 0.007 0.061 2209 Dihedral : 11.491 77.105 4825 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.53 % Favored : 91.02 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.84 (0.16), residues: 1582 helix: -3.10 (0.12), residues: 731 sheet: -3.82 (0.48), residues: 67 loop : -3.26 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 416 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 425 average time/residue: 0.3108 time to fit residues: 181.4293 Evaluate side-chains 227 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1218 time to fit residues: 3.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.0030 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 HIS A 63 ASN A 131 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 472 HIS A1114 ASN A1128 ASN A1154 ASN A1179 ASN A1241 ASN A1292 GLN A1297 ASN A1308 GLN A1331 GLN A1405 HIS A1665 ASN A1689 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12967 Z= 0.195 Angle : 0.685 13.162 17487 Z= 0.345 Chirality : 0.044 0.382 2015 Planarity : 0.005 0.046 2209 Dihedral : 5.927 35.676 1716 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.66 % Favored : 91.28 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.43 (0.18), residues: 1582 helix: -1.61 (0.16), residues: 745 sheet: -3.62 (0.49), residues: 63 loop : -2.86 (0.20), residues: 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 245 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 275 average time/residue: 0.2448 time to fit residues: 97.9228 Evaluate side-chains 219 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1187 time to fit residues: 6.0386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 158 optimal weight: 0.0020 chunk 130 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 overall best weight: 2.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A 906 ASN A1088 ASN A1111 ASN A1292 GLN A1358 HIS A1665 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 12967 Z= 0.297 Angle : 0.715 9.302 17487 Z= 0.361 Chirality : 0.046 0.400 2015 Planarity : 0.004 0.043 2209 Dihedral : 5.778 36.859 1716 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.87 (0.19), residues: 1582 helix: -1.14 (0.17), residues: 760 sheet: -3.61 (0.46), residues: 74 loop : -2.54 (0.22), residues: 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 253 average time/residue: 0.2715 time to fit residues: 100.3173 Evaluate side-chains 218 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1179 time to fit residues: 7.5430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 384 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12967 Z= 0.183 Angle : 0.636 9.284 17487 Z= 0.317 Chirality : 0.042 0.291 2015 Planarity : 0.004 0.043 2209 Dihedral : 5.373 35.277 1716 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.29 (0.20), residues: 1582 helix: -0.56 (0.18), residues: 755 sheet: -3.28 (0.48), residues: 74 loop : -2.35 (0.22), residues: 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 230 average time/residue: 0.2400 time to fit residues: 82.2329 Evaluate side-chains 201 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1191 time to fit residues: 5.6726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS A1162 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 12967 Z= 0.325 Angle : 0.708 9.020 17487 Z= 0.359 Chirality : 0.045 0.328 2015 Planarity : 0.004 0.047 2209 Dihedral : 5.609 36.174 1716 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.08 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.30 (0.20), residues: 1582 helix: -0.64 (0.18), residues: 772 sheet: -3.30 (0.48), residues: 72 loop : -2.32 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 1.480 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 239 average time/residue: 0.2615 time to fit residues: 90.1534 Evaluate side-chains 216 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1500 time to fit residues: 8.0107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1308 GLN ** A1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12967 Z= 0.184 Angle : 0.644 8.370 17487 Z= 0.322 Chirality : 0.043 0.477 2015 Planarity : 0.004 0.044 2209 Dihedral : 5.200 34.066 1716 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.91 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.82 (0.21), residues: 1582 helix: -0.10 (0.19), residues: 758 sheet: -2.87 (0.51), residues: 76 loop : -2.23 (0.22), residues: 748 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.471 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 230 average time/residue: 0.2507 time to fit residues: 84.2281 Evaluate side-chains 204 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1278 time to fit residues: 4.2706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 0.0870 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.0060 chunk 61 optimal weight: 6.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN ** A1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12967 Z= 0.177 Angle : 0.629 8.746 17487 Z= 0.314 Chirality : 0.042 0.421 2015 Planarity : 0.004 0.044 2209 Dihedral : 5.009 33.901 1716 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.09 % Favored : 91.85 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.59 (0.21), residues: 1582 helix: 0.13 (0.19), residues: 753 sheet: -2.93 (0.50), residues: 79 loop : -2.12 (0.23), residues: 750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.568 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 220 average time/residue: 0.2390 time to fit residues: 78.6864 Evaluate side-chains 200 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1180 time to fit residues: 3.7119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12967 Z= 0.186 Angle : 0.638 10.987 17487 Z= 0.316 Chirality : 0.043 0.388 2015 Planarity : 0.004 0.045 2209 Dihedral : 4.928 33.495 1716 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.51 (0.21), residues: 1582 helix: 0.25 (0.19), residues: 751 sheet: -2.72 (0.52), residues: 76 loop : -2.16 (0.22), residues: 755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.513 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 220 average time/residue: 0.2519 time to fit residues: 81.3449 Evaluate side-chains 204 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1248 time to fit residues: 3.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0030 chunk 148 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 0.0170 chunk 113 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 94 optimal weight: 5.9990 chunk 152 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 overall best weight: 0.6366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12967 Z= 0.176 Angle : 0.642 11.962 17487 Z= 0.317 Chirality : 0.043 0.357 2015 Planarity : 0.004 0.046 2209 Dihedral : 4.810 33.590 1716 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.97 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.38 (0.21), residues: 1582 helix: 0.37 (0.19), residues: 752 sheet: -2.72 (0.52), residues: 77 loop : -2.10 (0.23), residues: 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 1.417 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 211 average time/residue: 0.2401 time to fit residues: 75.3758 Evaluate side-chains 195 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1155 time to fit residues: 3.2348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 98 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12967 Z= 0.197 Angle : 0.658 12.539 17487 Z= 0.326 Chirality : 0.043 0.361 2015 Planarity : 0.004 0.045 2209 Dihedral : 4.847 33.111 1716 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.78 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1582 helix: 0.34 (0.19), residues: 755 sheet: -2.83 (0.50), residues: 80 loop : -2.04 (0.23), residues: 747 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.320 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.2396 time to fit residues: 70.1253 Evaluate side-chains 186 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.199708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169358 restraints weight = 15681.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.167467 restraints weight = 16464.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169133 restraints weight = 14466.530| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12967 Z= 0.184 Angle : 0.653 12.517 17487 Z= 0.323 Chirality : 0.043 0.357 2015 Planarity : 0.004 0.086 2209 Dihedral : 4.808 33.683 1716 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.97 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.28 (0.21), residues: 1582 helix: 0.38 (0.19), residues: 752 sheet: -2.62 (0.54), residues: 72 loop : -1.99 (0.23), residues: 758 =============================================================================== Job complete usr+sys time: 2621.36 seconds wall clock time: 48 minutes 37.11 seconds (2917.11 seconds total)