Starting phenix.real_space_refine on Mon Apr 8 06:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/04_2024/7vh3_31985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/04_2024/7vh3_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_31985/04_2024/7vh3_31985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/04_2024/7vh3_31985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/04_2024/7vh3_31985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh3_31985/04_2024/7vh3_31985.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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 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. 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-5288/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: 6.84, per 1000 atoms: 0.54 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: 4.47 Conformation dependent library (CDL) restraints added in 2.1 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: 1.46 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: 4.56 Time building geometry restraints manager: 4.89 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 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: 0.730 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: 3.500 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.010 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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 % Allowed : 6.45 % Favored : 92.64 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1680 HIS 0.008 0.002 HIS A 647 PHE 0.027 0.003 PHE A1386 TYR 0.026 0.002 TYR A 555 ARG 0.009 0.001 ARG A 636 *********************** 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 : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.6380 (t80) cc_final: 0.6062 (t80) REVERT: A 329 SER cc_start: 0.6708 (p) cc_final: 0.6332 (t) REVERT: A 376 ARG cc_start: 0.7070 (mmm-85) cc_final: 0.6738 (mmm-85) REVERT: A 640 MET cc_start: 0.7231 (mtm) cc_final: 0.7015 (mtm) REVERT: A 652 ILE cc_start: 0.8361 (mm) cc_final: 0.8104 (mm) REVERT: A 714 LEU cc_start: 0.8133 (tt) cc_final: 0.7622 (mp) REVERT: A 1103 THR cc_start: 0.6834 (m) cc_final: 0.6528 (p) REVERT: A 1141 MET cc_start: 0.8557 (mmt) cc_final: 0.8101 (mmt) REVERT: A 1144 LEU cc_start: 0.8228 (mt) cc_final: 0.7965 (mt) REVERT: A 1162 ASN cc_start: 0.6247 (p0) cc_final: 0.5388 (m110) REVERT: A 1309 PHE cc_start: 0.6627 (t80) cc_final: 0.6363 (t80) REVERT: A 1321 ILE cc_start: 0.7757 (pt) cc_final: 0.7433 (tp) outliers start: 13 outliers final: 7 residues processed: 425 average time/residue: 0.3013 time to fit residues: 175.3704 Evaluate side-chains 232 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 1560 LEU 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: 0.0010 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.0070 chunk 93 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- 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: 0.6962 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12967 Z= 0.189 Angle : 0.674 12.606 17487 Z= 0.340 Chirality : 0.043 0.178 2015 Planarity : 0.005 0.044 2209 Dihedral : 6.435 57.731 1728 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.28 % Favored : 91.66 % Rotamer: Outliers : 4.02 % Allowed : 13.12 % Favored : 82.86 % 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: -3.38 (0.19), residues: 1582 helix: -1.56 (0.17), residues: 741 sheet: -3.68 (0.48), residues: 65 loop : -2.83 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1230 HIS 0.003 0.001 HIS A 647 PHE 0.024 0.002 PHE A1148 TYR 0.015 0.002 TYR A 214 ARG 0.007 0.000 ARG A1796 *********************** 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 304 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 246 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.6644 (p) cc_final: 0.6273 (t) REVERT: A 527 GLU cc_start: 0.7276 (pp20) cc_final: 0.6399 (pm20) REVERT: A 714 LEU cc_start: 0.8129 (tt) cc_final: 0.7592 (mp) REVERT: A 848 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6604 (ttm) REVERT: A 1021 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 1141 MET cc_start: 0.8641 (mmt) cc_final: 0.8178 (mmt) REVERT: A 1162 ASN cc_start: 0.5955 (p0) cc_final: 0.5168 (m110) REVERT: A 1290 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6587 (tmm) REVERT: A 1307 GLU cc_start: 0.7814 (tp30) cc_final: 0.7574 (tp30) REVERT: A 1321 ILE cc_start: 0.7647 (pt) cc_final: 0.7402 (tp) REVERT: A 1375 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7989 (mt) REVERT: A 1495 ARG cc_start: 0.7263 (mtm180) cc_final: 0.6950 (mtp180) REVERT: A 1663 TYR cc_start: 0.6448 (m-80) cc_final: 0.5984 (m-10) outliers start: 58 outliers final: 24 residues processed: 282 average time/residue: 0.2665 time to fit residues: 110.7713 Evaluate side-chains 232 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1651 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 146 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.2102 ------------------------------------------------------------------------------- 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 A 522 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS A 754 ASN A 906 ASN A1088 ASN A1292 GLN A1358 HIS A1665 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12967 Z= 0.307 Angle : 0.710 11.525 17487 Z= 0.359 Chirality : 0.044 0.182 2015 Planarity : 0.004 0.043 2209 Dihedral : 6.257 55.504 1725 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer: Outliers : 4.58 % Allowed : 16.17 % Favored : 79.25 % 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: -2.94 (0.19), residues: 1582 helix: -1.19 (0.17), residues: 764 sheet: -3.73 (0.44), residues: 74 loop : -2.58 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1230 HIS 0.006 0.001 HIS A 276 PHE 0.021 0.002 PHE A1148 TYR 0.022 0.002 TYR A 555 ARG 0.006 0.001 ARG A 376 *********************** 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 290 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 224 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6981 (mm) REVERT: A 329 SER cc_start: 0.6803 (p) cc_final: 0.6437 (t) REVERT: A 376 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6697 (mmm-85) REVERT: A 714 LEU cc_start: 0.8277 (tt) cc_final: 0.7685 (mp) REVERT: A 741 ASN cc_start: 0.7005 (p0) cc_final: 0.6729 (p0) REVERT: A 848 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6912 (ttm) REVERT: A 1021 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 1030 TYR cc_start: 0.7991 (m-10) cc_final: 0.7673 (m-80) REVERT: A 1097 TYR cc_start: 0.6494 (t80) cc_final: 0.6293 (t80) REVERT: A 1141 MET cc_start: 0.8657 (mmt) cc_final: 0.8248 (mmt) REVERT: A 1162 ASN cc_start: 0.6646 (p0) cc_final: 0.5934 (m-40) REVERT: A 1321 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7459 (tp) REVERT: A 1495 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7121 (mtp180) REVERT: A 1662 ILE cc_start: 0.6749 (mm) cc_final: 0.6511 (mm) REVERT: A 1663 TYR cc_start: 0.6645 (m-80) cc_final: 0.6094 (m-10) outliers start: 66 outliers final: 40 residues processed: 266 average time/residue: 0.2495 time to fit residues: 97.5244 Evaluate side-chains 234 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0060 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.0798 ------------------------------------------------------------------------------- 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** A1665 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12967 Z= 0.202 Angle : 0.636 10.071 17487 Z= 0.320 Chirality : 0.041 0.164 2015 Planarity : 0.004 0.043 2209 Dihedral : 5.816 51.499 1723 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.91 % Rotamer: Outliers : 4.86 % Allowed : 16.72 % Favored : 78.42 % 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: -2.33 (0.20), residues: 1582 helix: -0.53 (0.18), residues: 748 sheet: -3.47 (0.46), residues: 74 loop : -2.42 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1230 HIS 0.004 0.001 HIS A 647 PHE 0.028 0.002 PHE A 352 TYR 0.015 0.001 TYR A 555 ARG 0.006 0.000 ARG A1438 *********************** 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 286 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 216 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6993 (mm) REVERT: A 224 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 329 SER cc_start: 0.6831 (p) cc_final: 0.6447 (t) REVERT: A 714 LEU cc_start: 0.8286 (tt) cc_final: 0.7706 (mp) REVERT: A 848 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6850 (ttm) REVERT: A 1030 TYR cc_start: 0.7911 (m-10) cc_final: 0.7596 (m-80) REVERT: A 1141 MET cc_start: 0.8611 (mmt) cc_final: 0.8246 (mmt) REVERT: A 1162 ASN cc_start: 0.6215 (p0) cc_final: 0.5900 (m-40) REVERT: A 1290 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6386 (tmm) REVERT: A 1321 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7496 (tp) REVERT: A 1385 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7787 (mtp180) REVERT: A 1495 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7001 (mtm110) REVERT: A 1663 TYR cc_start: 0.6525 (m-80) cc_final: 0.6136 (m-10) outliers start: 70 outliers final: 45 residues processed: 263 average time/residue: 0.2344 time to fit residues: 91.6559 Evaluate side-chains 247 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 195 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1495 ARG Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1810 LEU 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: 3.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 A1665 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: 0.7225 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12967 Z= 0.279 Angle : 0.670 8.521 17487 Z= 0.341 Chirality : 0.043 0.182 2015 Planarity : 0.004 0.046 2209 Dihedral : 5.720 46.156 1721 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 5.48 % Allowed : 17.63 % Favored : 76.89 % 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: -2.22 (0.20), residues: 1582 helix: -0.52 (0.18), residues: 775 sheet: -3.62 (0.44), residues: 75 loop : -2.28 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.005 0.001 HIS A 276 PHE 0.026 0.002 PHE A1148 TYR 0.017 0.002 TYR A 555 ARG 0.007 0.001 ARG A 376 *********************** 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 291 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 212 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7091 (mm) REVERT: A 110 ASP cc_start: 0.4708 (OUTLIER) cc_final: 0.4273 (m-30) REVERT: A 224 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 329 SER cc_start: 0.6943 (p) cc_final: 0.6597 (t) REVERT: A 660 LYS cc_start: 0.8187 (tppt) cc_final: 0.7947 (mmtm) REVERT: A 714 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 838 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 848 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6850 (ttm) REVERT: A 870 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.6952 (tt) REVERT: A 1030 TYR cc_start: 0.8017 (m-10) cc_final: 0.7735 (m-80) REVERT: A 1141 MET cc_start: 0.8627 (mmt) cc_final: 0.8308 (mmt) REVERT: A 1230 TRP cc_start: 0.7724 (m-10) cc_final: 0.7422 (m-10) REVERT: A 1290 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6564 (tmm) REVERT: A 1321 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 1434 LYS cc_start: 0.7667 (tttm) cc_final: 0.7147 (tttt) REVERT: A 1438 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7553 (mtt180) REVERT: A 1495 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7126 (mtp180) REVERT: A 1663 TYR cc_start: 0.6525 (m-80) cc_final: 0.6129 (m-10) outliers start: 79 outliers final: 53 residues processed: 263 average time/residue: 0.2526 time to fit residues: 97.2962 Evaluate side-chains 260 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 197 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1495 ARG Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 chunk 150 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN A1665 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: 0.7127 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12967 Z= 0.180 Angle : 0.617 8.699 17487 Z= 0.311 Chirality : 0.041 0.160 2015 Planarity : 0.004 0.044 2209 Dihedral : 5.370 39.391 1721 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.16 % Rotamer: Outliers : 4.51 % Allowed : 19.50 % Favored : 75.99 % 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: -1.80 (0.21), residues: 1582 helix: -0.06 (0.19), residues: 752 sheet: -3.18 (0.48), residues: 74 loop : -2.20 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 429 HIS 0.005 0.001 HIS A 647 PHE 0.029 0.002 PHE A 352 TYR 0.016 0.001 TYR A 572 ARG 0.005 0.000 ARG A 376 *********************** 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 280 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7061 (mm) REVERT: A 224 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (tt) REVERT: A 329 SER cc_start: 0.6757 (p) cc_final: 0.6417 (t) REVERT: A 485 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7519 (tpt170) REVERT: A 714 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7736 (mp) REVERT: A 838 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 848 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6669 (ttm) REVERT: A 870 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.6998 (tt) REVERT: A 1141 MET cc_start: 0.8591 (mmt) cc_final: 0.8203 (mmt) REVERT: A 1230 TRP cc_start: 0.7583 (m-10) cc_final: 0.7359 (m-10) REVERT: A 1270 PHE cc_start: 0.6656 (t80) cc_final: 0.6456 (t80) REVERT: A 1290 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6573 (tmm) REVERT: A 1375 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 1385 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7610 (mtp180) REVERT: A 1663 TYR cc_start: 0.6362 (m-80) cc_final: 0.6045 (m-10) outliers start: 65 outliers final: 46 residues processed: 254 average time/residue: 0.2340 time to fit residues: 88.3552 Evaluate side-chains 258 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 203 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1805 GLN Chi-restraints excluded: chain A residue 1810 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4419 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= 0.193 Angle : 0.617 7.972 17487 Z= 0.311 Chirality : 0.041 0.167 2015 Planarity : 0.004 0.044 2209 Dihedral : 5.244 37.443 1721 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.85 % Favored : 91.09 % Rotamer: Outliers : 4.65 % Allowed : 19.99 % Favored : 75.36 % 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: -1.68 (0.21), residues: 1582 helix: 0.08 (0.19), residues: 752 sheet: -3.27 (0.47), residues: 77 loop : -2.16 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 429 HIS 0.004 0.001 HIS A 647 PHE 0.028 0.001 PHE A1148 TYR 0.026 0.001 TYR A1030 ARG 0.007 0.000 ARG A 376 *********************** 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 282 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 215 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7103 (mm) REVERT: A 224 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7925 (tt) REVERT: A 329 SER cc_start: 0.6884 (p) cc_final: 0.6544 (t) REVERT: A 485 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7516 (tpt170) REVERT: A 710 THR cc_start: 0.7486 (p) cc_final: 0.7280 (p) REVERT: A 714 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 869 ILE cc_start: 0.8303 (mt) cc_final: 0.8062 (mm) REVERT: A 870 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7387 (tt) REVERT: A 1141 MET cc_start: 0.8603 (mmt) cc_final: 0.8186 (mmt) REVERT: A 1230 TRP cc_start: 0.7585 (m-10) cc_final: 0.7358 (m-10) REVERT: A 1290 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6561 (tmm) REVERT: A 1321 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7434 (tp) REVERT: A 1375 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 1663 TYR cc_start: 0.6298 (m-80) cc_final: 0.5979 (m-10) outliers start: 67 outliers final: 48 residues processed: 257 average time/residue: 0.2448 time to fit residues: 92.8036 Evaluate side-chains 262 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 207 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1805 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 148 optimal weight: 0.4980 chunk 135 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4538 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= 0.192 Angle : 0.629 9.473 17487 Z= 0.316 Chirality : 0.042 0.259 2015 Planarity : 0.004 0.044 2209 Dihedral : 5.194 36.499 1721 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.84 % Favored : 92.10 % Rotamer: Outliers : 4.65 % Allowed : 20.19 % Favored : 75.16 % 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: 0.15 (0.19), residues: 761 sheet: -3.12 (0.48), residues: 74 loop : -2.15 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 429 HIS 0.004 0.001 HIS A 647 PHE 0.030 0.002 PHE A 352 TYR 0.027 0.001 TYR A1030 ARG 0.010 0.000 ARG A 376 *********************** 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 281 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 214 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7078 (mm) REVERT: A 329 SER cc_start: 0.6883 (p) cc_final: 0.6548 (t) REVERT: A 485 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7384 (tpt170) REVERT: A 710 THR cc_start: 0.7544 (p) cc_final: 0.7317 (p) REVERT: A 714 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 869 ILE cc_start: 0.8222 (mt) cc_final: 0.7950 (mm) REVERT: A 870 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7041 (tt) REVERT: A 1021 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 1141 MET cc_start: 0.8602 (mmt) cc_final: 0.8174 (mmt) REVERT: A 1230 TRP cc_start: 0.7587 (m-10) cc_final: 0.7366 (m-10) REVERT: A 1290 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6354 (tmm) REVERT: A 1321 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7420 (tp) REVERT: A 1663 TYR cc_start: 0.6261 (m-80) cc_final: 0.5950 (m-10) outliers start: 67 outliers final: 50 residues processed: 257 average time/residue: 0.2337 time to fit residues: 89.3210 Evaluate side-chains 264 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 209 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1681 ASP Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1805 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 6.9990 chunk 148 optimal weight: 0.0980 chunk 87 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 326 HIS ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12967 Z= 0.286 Angle : 0.680 11.397 17487 Z= 0.343 Chirality : 0.044 0.211 2015 Planarity : 0.004 0.043 2209 Dihedral : 5.461 43.849 1721 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.42 % Favored : 90.52 % Rotamer: Outliers : 5.00 % Allowed : 20.33 % Favored : 74.67 % 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: -1.73 (0.21), residues: 1582 helix: -0.02 (0.19), residues: 760 sheet: -3.47 (0.46), residues: 74 loop : -2.11 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.005 0.001 HIS A 276 PHE 0.028 0.002 PHE A1148 TYR 0.031 0.002 TYR A1030 ARG 0.008 0.001 ARG A 376 *********************** 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 290 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 218 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7253 (mm) REVERT: A 329 SER cc_start: 0.6970 (p) cc_final: 0.6644 (t) REVERT: A 455 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6448 (ttt180) REVERT: A 714 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 869 ILE cc_start: 0.8340 (mt) cc_final: 0.8070 (mm) REVERT: A 1141 MET cc_start: 0.8618 (mmt) cc_final: 0.8172 (mmt) REVERT: A 1230 TRP cc_start: 0.7674 (m-10) cc_final: 0.7404 (m-10) REVERT: A 1290 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6714 (tmm) REVERT: A 1321 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 1385 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7816 (mtp180) REVERT: A 1663 TYR cc_start: 0.6387 (m-80) cc_final: 0.6036 (m-10) REVERT: A 1696 TRP cc_start: 0.6501 (p-90) cc_final: 0.5540 (p-90) REVERT: A 1782 MET cc_start: 0.4627 (ptm) cc_final: 0.4250 (ptm) outliers start: 72 outliers final: 58 residues processed: 265 average time/residue: 0.2341 time to fit residues: 92.3418 Evaluate side-chains 263 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1385 ARG Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1495 ARG Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1681 ASP Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1805 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 147 optimal weight: 0.0270 chunk 127 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- 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 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1665 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12967 Z= 0.265 Angle : 0.693 10.890 17487 Z= 0.349 Chirality : 0.043 0.239 2015 Planarity : 0.004 0.043 2209 Dihedral : 5.483 45.264 1721 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.98 % Favored : 90.96 % Rotamer: Outliers : 4.37 % Allowed : 21.37 % Favored : 74.25 % 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: -1.74 (0.21), residues: 1582 helix: -0.03 (0.19), residues: 757 sheet: -3.29 (0.46), residues: 78 loop : -2.13 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.004 0.001 HIS A 276 PHE 0.031 0.002 PHE A1148 TYR 0.014 0.002 TYR A 910 ARG 0.010 0.001 ARG A 376 ********************** 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 272 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 209 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7235 (mm) REVERT: A 329 SER cc_start: 0.6947 (p) cc_final: 0.6625 (t) REVERT: A 455 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6405 (ttt180) REVERT: A 714 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 869 ILE cc_start: 0.8487 (mt) cc_final: 0.8227 (mm) REVERT: A 1141 MET cc_start: 0.8629 (mmt) cc_final: 0.8177 (mmt) REVERT: A 1230 TRP cc_start: 0.7675 (m-10) cc_final: 0.7402 (m-10) REVERT: A 1290 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6496 (tmm) REVERT: A 1321 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7586 (tp) REVERT: A 1663 TYR cc_start: 0.6446 (m-80) cc_final: 0.6081 (m-10) REVERT: A 1696 TRP cc_start: 0.6588 (p-90) cc_final: 0.5615 (p-90) outliers start: 63 outliers final: 53 residues processed: 252 average time/residue: 0.2275 time to fit residues: 85.7087 Evaluate side-chains 259 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 201 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1286 SER Chi-restraints excluded: chain A residue 1289 ASP Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1550 VAL Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1678 ILE Chi-restraints excluded: chain A residue 1681 ASP Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1805 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 112 optimal weight: 0.0270 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 0.0010 overall best weight: 0.4444 ------------------------------------------------------------------------------- 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 859 ASN ** A1711 ASN ** 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 = 0.4342 r_free = 0.4342 target = 0.200425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.171811 restraints weight = 15680.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170115 restraints weight = 16475.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171486 restraints weight = 15241.436| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12967 Z= 0.170 Angle : 0.643 10.897 17487 Z= 0.321 Chirality : 0.041 0.171 2015 Planarity : 0.004 0.045 2209 Dihedral : 5.140 43.239 1721 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 3.26 % Allowed : 22.41 % Favored : 74.32 % 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: -1.43 (0.21), residues: 1582 helix: 0.28 (0.19), residues: 755 sheet: -3.10 (0.47), residues: 75 loop : -2.04 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 429 HIS 0.005 0.001 HIS A 647 PHE 0.029 0.001 PHE A1148 TYR 0.017 0.001 TYR A 910 ARG 0.009 0.000 ARG A 376 =============================================================================== Job complete usr+sys time: 2768.19 seconds wall clock time: 51 minutes 30.29 seconds (3090.29 seconds total)