Starting phenix.real_space_refine
on Thu Sep 26 10:16:57 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo9_32643/09_2024/7wo9_32643.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo9_32643/09_2024/7wo9_32643.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo9_32643/09_2024/7wo9_32643.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo9_32643/09_2024/7wo9_32643.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo9_32643/09_2024/7wo9_32643.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo9_32643/09_2024/7wo9_32643.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.046
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      29      5.16       5
     C    8262      2.51       5
     N    2036      2.21       5
     O    2416      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 12743
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1581, 12743
          Classifications: {'peptide': 1581}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 44, 'TRANS': 1536}
          Chain breaks: 5
  Time building chain proxies: 0.00, per 1000 atoms: 0.00
  Number of scatterers: 12743
  At special positions: 0
  Unit cell: (78.156, 106.212, 187.708, 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      29     16.00
     O    2416      8.00
     N    2036      7.00
     C    8262      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.28
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3086

  Finding SS restraints...
    Secondary structure from input PDB file:
      91 helices and 3 sheets defined
      75.1% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 25
    Processing helix  chain 'A' and resid 26 through 27
      No H-bonds generated for 'chain 'A' and resid 26 through 27'
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 33 through 47
    Processing helix  chain 'A' and resid 70 through 80
    Processing helix  chain 'A' and resid 86 through 92
    Processing helix  chain 'A' and resid 94 through 119
      removed outlier: 3.854A  pdb=" N   LEU A 110 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 122
      No H-bonds generated for 'chain 'A' and resid 120 through 122'
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 3.555A  pdb=" N   PHE A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A 130 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 151
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 167 through 199
    Processing helix  chain 'A' and resid 205 through 219
      removed outlier: 4.009A  pdb=" N   GLN A 217 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
    Processing helix  chain 'A' and resid 247 through 273
      removed outlier: 4.983A  pdb=" N   LEU A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER A 259 " --> pdb=" O   GLU A 255 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 291
    Processing helix  chain 'A' and resid 293 through 308
    Processing helix  chain 'A' and resid 318 through 336
      removed outlier: 3.609A  pdb=" N   HIS A 322 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 327 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 356
      removed outlier: 4.399A  pdb=" N   PHE A 349 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 372 through 387
      removed outlier: 4.219A  pdb=" N   THR A 376 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 390
      No H-bonds generated for 'chain 'A' and resid 388 through 390'
    Processing helix  chain 'A' and resid 393 through 405
      removed outlier: 3.618A  pdb=" N   SER A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 417
    Processing helix  chain 'A' and resid 418 through 431
      removed outlier: 3.578A  pdb=" N   ILE A 427 " --> pdb=" O   LYS A 423 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE A 428 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 446
    Processing helix  chain 'A' and resid 449 through 459
      removed outlier: 4.414A  pdb=" N   ASP A 459 " --> pdb=" O   PHE A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
      removed outlier: 3.787A  pdb=" N   ASP A 472 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 579
      removed outlier: 3.922A  pdb=" N   LEU A 564 " --> pdb=" O   ASN A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 602
    Processing helix  chain 'A' and resid 607 through 619
      removed outlier: 3.506A  pdb=" N   SER A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 649
      removed outlier: 3.630A  pdb=" N   VAL A 637 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 665
      removed outlier: 3.634A  pdb=" N   THR A 665 " --> pdb=" O   MET A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 679
      removed outlier: 3.846A  pdb=" N   VAL A 672 " --> pdb=" O   TYR A 668 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 698
    Processing helix  chain 'A' and resid 698 through 703
    Processing helix  chain 'A' and resid 705 through 723
    Processing helix  chain 'A' and resid 731 through 751
      removed outlier: 3.596A  pdb=" N   LYS A 735 " --> pdb=" O   SER A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 756
    Processing helix  chain 'A' and resid 760 through 784
      removed outlier: 4.089A  pdb=" N   LYS A 764 " --> pdb=" O   ASN A 760 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A 765 " --> pdb=" O   PHE A 761 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   HIS A 770 " --> pdb=" O   GLU A 766 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR A 776 " --> pdb=" O   THR A 772 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASP A 777 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 782 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A 784 " --> pdb=" O   HIS A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 807
    Processing helix  chain 'A' and resid 814 through 825
      removed outlier: 4.090A  pdb=" N   ASN A 818 " --> pdb=" O   ASP A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 828
      No H-bonds generated for 'chain 'A' and resid 826 through 828'
    Processing helix  chain 'A' and resid 829 through 836
    Processing helix  chain 'A' and resid 842 through 864
    Processing helix  chain 'A' and resid 871 through 880
      removed outlier: 3.628A  pdb=" N   LYS A 875 " --> pdb=" O   SER A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 889
      removed outlier: 3.520A  pdb=" N   ASP A 886 " --> pdb=" O   SER A 882 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 887 " --> pdb=" O   LYS A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 910
      removed outlier: 3.675A  pdb=" N   ILE A 900 " --> pdb=" O   PHE A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 924
    Processing helix  chain 'A' and resid 924 through 940
      removed outlier: 3.648A  pdb=" N   MET A 929 " --> pdb=" O   GLU A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 962
    Processing helix  chain 'A' and resid 964 through 974
    Processing helix  chain 'A' and resid 979 through 983
    Processing helix  chain 'A' and resid 989 through 992
    Processing helix  chain 'A' and resid 993 through 1003
      removed outlier: 4.062A  pdb=" N   VAL A 997 " --> pdb=" O   SER A 993 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   LEU A1003 " --> pdb=" O   GLN A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1026
      removed outlier: 3.986A  pdb=" N   THR A1026 " --> pdb=" O   TYR A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1050
    Processing helix  chain 'A' and resid 1051 through 1054
    Processing helix  chain 'A' and resid 1061 through 1089
      removed outlier: 3.546A  pdb=" N   ARG A1077 " --> pdb=" O   LYS A1073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1101
    Processing helix  chain 'A' and resid 1104 through 1110
      removed outlier: 3.748A  pdb=" N   LEU A1108 " --> pdb=" O   ASP A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1111 through 1114
      removed outlier: 3.668A  pdb=" N   GLN A1114 " --> pdb=" O   HIS A1111 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1111 through 1114'
    Processing helix  chain 'A' and resid 1119 through 1134
      removed outlier: 3.781A  pdb=" N   ASN A1127 " --> pdb=" O   HIS A1123 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS A1131 " --> pdb=" O   ASN A1127 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLU A1132 " --> pdb=" O   LEU A1128 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A1133 " --> pdb=" O   LYS A1129 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TRP A1134 " --> pdb=" O   PHE A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1143
    Processing helix  chain 'A' and resid 1159 through 1167
    Processing helix  chain 'A' and resid 1170 through 1175
    Processing helix  chain 'A' and resid 1182 through 1218
      removed outlier: 3.549A  pdb=" N   LEU A1192 " --> pdb=" O   THR A1188 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A1194 " --> pdb=" O   ALA A1190 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLN A1195 " --> pdb=" O   SER A1191 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ARG A1217 " --> pdb=" O   THR A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1223 through 1239
      removed outlier: 4.067A  pdb=" N   VAL A1227 " --> pdb=" O   ASN A1223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1268
      removed outlier: 3.783A  pdb=" N   PHE A1265 " --> pdb=" O   ILE A1261 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LYS A1266 " --> pdb=" O   LEU A1262 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LEU A1267 " --> pdb=" O   TYR A1263 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER A1268 " --> pdb=" O   SER A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1273 through 1289
      removed outlier: 3.792A  pdb=" N   ILE A1277 " --> pdb=" O   LYS A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1298 through 1304
      removed outlier: 4.068A  pdb=" N   SER A1302 " --> pdb=" O   ASN A1298 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A1303 " --> pdb=" O   ILE A1299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1307
      No H-bonds generated for 'chain 'A' and resid 1305 through 1307'
    Processing helix  chain 'A' and resid 1308 through 1319
    Processing helix  chain 'A' and resid 1328 through 1360
      removed outlier: 3.924A  pdb=" N   LYS A1346 " --> pdb=" O   LEU A1342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1379 through 1384
      removed outlier: 3.702A  pdb=" N   ASP A1384 " --> pdb=" O   ASP A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1387 through 1397
    Processing helix  chain 'A' and resid 1401 through 1416
    Processing helix  chain 'A' and resid 1418 through 1431
    Processing helix  chain 'A' and resid 1439 through 1452
      removed outlier: 4.027A  pdb=" N   THR A1443 " --> pdb=" O   LEU A1439 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A1444 " --> pdb=" O   GLY A1440 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   THR A1445 " --> pdb=" O   GLN A1441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1453 through 1462
      removed outlier: 3.543A  pdb=" N   ASN A1462 " --> pdb=" O   ALA A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1464 through 1471
      removed outlier: 3.698A  pdb=" N   VAL A1468 " --> pdb=" O   GLY A1464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1472 through 1480
    Processing helix  chain 'A' and resid 1488 through 1510
    Processing helix  chain 'A' and resid 1514 through 1525
    Processing helix  chain 'A' and resid 1525 through 1539
      removed outlier: 3.727A  pdb=" N   ILE A1529 " --> pdb=" O   PHE A1525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1544 through 1558
    Processing helix  chain 'A' and resid 1559 through 1564
      removed outlier: 3.686A  pdb=" N   LEU A1564 " --> pdb=" O   MET A1560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1606
      removed outlier: 3.760A  pdb=" N   LYS A1595 " --> pdb=" O   SER A1591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1608 through 1616
    Processing helix  chain 'A' and resid 1620 through 1629
    Processing helix  chain 'A' and resid 1632 through 1655
    Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276
    Processing sheet with id=AA2, first strand: chain 'A' and resid 460 through 466
      removed outlier: 5.492A  pdb=" N   TYR A 557 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   ALA A 464 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   PHE A 555 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   THR A 466 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   ILE A 553 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A 556 " --> pdb=" O   LYS A 525 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   LYS A 525 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 505

    782 hydrogen bonds defined for protein.
    2295 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: 5.02

  Time building geometry restraints manager: 2.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 4003
        1.34 -     1.46: 1874
        1.46 -     1.57: 7054
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 12977
  Sorted by residual:
  bond pdb=" N   LEU A 583 "
       pdb=" CA  LEU A 583 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.25e-02 6.40e+03 7.20e+00
  bond pdb=" N   ASP A 584 "
       pdb=" CA  ASP A 584 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.23e-02 6.61e+03 6.35e+00
  bond pdb=" N   ASP A 585 "
       pdb=" CA  ASP A 585 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.27e+00
  bond pdb=" N   LYS A 716 "
       pdb=" CA  LYS A 716 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.10e+00
  bond pdb=" N   LEU A 773 "
       pdb=" CA  LEU A 773 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.90e+00
  ... (remaining 12972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 17254
        1.50 -     3.00: 251
        3.00 -     4.50: 45
        4.50 -     6.01: 24
        6.01 -     7.51: 5
  Bond angle restraints: 17579
  Sorted by residual:
  angle pdb=" CA  VAL A1398 "
        pdb=" C   VAL A1398 "
        pdb=" O   VAL A1398 "
      ideal   model   delta    sigma   weight residual
     120.78  116.80    3.98 1.25e+00 6.40e-01 1.01e+01
  angle pdb=" OG1 THR A1028 "
        pdb=" CB  THR A1028 "
        pdb=" CG2 THR A1028 "
      ideal   model   delta    sigma   weight residual
     109.30  103.23    6.07 2.00e+00 2.50e-01 9.22e+00
  angle pdb=" CA  TRP A1495 "
        pdb=" CB  TRP A1495 "
        pdb=" CG  TRP A1495 "
      ideal   model   delta    sigma   weight residual
     113.60  119.25   -5.65 1.90e+00 2.77e-01 8.84e+00
  angle pdb=" C   THR A1417 "
        pdb=" N   LEU A1418 "
        pdb=" CA  LEU A1418 "
      ideal   model   delta    sigma   weight residual
     121.54  127.16   -5.62 1.91e+00 2.74e-01 8.67e+00
  angle pdb=" C   GLN A1558 "
        pdb=" N   LYS A1559 "
        pdb=" CA  LYS A1559 "
      ideal   model   delta    sigma   weight residual
     121.54  127.07   -5.53 1.91e+00 2.74e-01 8.37e+00
  ... (remaining 17574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 7100
       18.00 -    36.00: 671
       36.00 -    54.00: 88
       54.00 -    72.00: 16
       72.00 -    90.00: 9
  Dihedral angle restraints: 7884
    sinusoidal: 3176
      harmonic: 4708
  Sorted by residual:
  dihedral pdb=" CB  GLU A1185 "
           pdb=" CG  GLU A1185 "
           pdb=" CD  GLU A1185 "
           pdb=" OE1 GLU A1185 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -90.00   90.00     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  GLU A 510 "
           pdb=" CG  GLU A 510 "
           pdb=" CD  GLU A 510 "
           pdb=" OE1 GLU A 510 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.13  -89.13     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CA  ASP A 153 "
           pdb=" CB  ASP A 153 "
           pdb=" CG  ASP A 153 "
           pdb=" OD1 ASP A 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.27   55.27     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 7881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1462
       0.034 -    0.068: 496
       0.068 -    0.101: 113
       0.101 -    0.135: 32
       0.135 -    0.169: 5
  Chirality restraints: 2108
  Sorted by residual:
  chirality pdb=" CB  THR A1028 "
            pdb=" CA  THR A1028 "
            pdb=" OG1 THR A1028 "
            pdb=" CG2 THR A1028 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CA  ILE A 785 "
            pdb=" N   ILE A 785 "
            pdb=" C   ILE A 785 "
            pdb=" CB  ILE A 785 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  LEU A 583 "
            pdb=" N   LEU A 583 "
            pdb=" C   LEU A 583 "
            pdb=" CB  LEU A 583 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 2105 not shown)

  Planarity restraints: 2189
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1495 "    0.028 2.00e-02 2.50e+03   2.64e-02 1.74e+01
        pdb=" CG  TRP A1495 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1495 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1495 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1495 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1495 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1495 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1495 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1495 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1495 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1309 "   -0.066 5.00e-02 4.00e+02   9.84e-02 1.55e+01
        pdb=" N   PRO A1310 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A1310 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A1310 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 507 "    0.043 5.00e-02 4.00e+02   6.51e-02 6.78e+00
        pdb=" N   PRO A 508 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 508 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 508 "    0.036 5.00e-02 4.00e+02
  ... (remaining 2186 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2133
        2.76 -     3.30: 12699
        3.30 -     3.83: 20740
        3.83 -     4.37: 23748
        4.37 -     4.90: 41866
  Nonbonded interactions: 101186
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 780 "
            pdb=" OG1 THR A 784 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" NH1 ARG A 333 "
            pdb=" O   PHE A 341 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   ALA A1428 "
            pdb=" NH2 ARG A1432 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   LEU A1589 "
            pdb=" NZ  LYS A1595 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG  SER A 826 "
            pdb=" OH  TYR A 844 "
     model   vdw
     2.290 3.040
  ... (remaining 101181 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             39.980
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     21.450
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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      :  0.002   0.042  12977  Z= 0.151
  Angle     :  0.504   7.507  17579  Z= 0.270
  Chirality :  0.037   0.169   2108
  Planarity :  0.004   0.098   2189
  Dihedral  : 13.974  89.997   4798
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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:  1.49 (0.22), residues: 1569
  helix:  1.68 (0.16), residues: 1079
  sheet:  0.54 (0.91), residues: 36
  loop : -0.62 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP A1495 
 HIS   0.002   0.001   HIS A 729 
 PHE   0.028   0.001   PHE A1285 
 TYR   0.019   0.001   TYR A 323 
 ARG   0.006   0.000   ARG A1313 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 1.0832
  time to fit residues: 127.8568
Evaluate side-chains
  71 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 75 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0970
   chunk 143 optimal weight:    6.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
A 363 ASN
A 388 ASN
A 729 HIS
A 788 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12977  Z= 0.284
  Angle     :  0.581   7.668  17579  Z= 0.301
  Chirality :  0.040   0.180   2108
  Planarity :  0.004   0.075   2189
  Dihedral  :  4.100  27.789   1656
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.25 %
    Favored  : 92.75 %
  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:  1.30 (0.22), residues: 1569
  helix:  1.57 (0.16), residues: 1076
  sheet:  0.51 (0.90), residues: 37
  loop : -0.77 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A1495 
 HIS   0.006   0.001   HIS A 318 
 PHE   0.023   0.002   PHE A1605 
 TYR   0.026   0.002   TYR A1260 
 ARG   0.006   0.001   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  589 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6466 (mm-30)
REVERT: A 1170 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.7016 (t70)
  outliers start: 15
  outliers final: 6
  residues processed: 87
  average time/residue: 1.1046
  time to fit residues: 107.2464
Evaluate side-chains
  79 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  215 GLN
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1152 GLU
Chi-restraints excluded: chain A residue 1170 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0070
   chunk 119 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0070
   chunk 39 optimal weight:    3.9990
   chunk 143 optimal weight:    0.0670
   chunk 155 optimal weight:    7.9990
   chunk 128 optimal weight:    0.9990
   chunk 142 optimal weight:   50.0000
   chunk 49 optimal weight:    0.0870
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.1932

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN
A 729 HIS
A1151 ASN
A1492 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12977  Z= 0.123
  Angle     :  0.461   7.693  17579  Z= 0.240
  Chirality :  0.036   0.147   2108
  Planarity :  0.003   0.060   2189
  Dihedral  :  3.834  28.024   1656
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.93 %
    Favored  : 90.46 %
  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:  1.81 (0.22), residues: 1569
  helix:  2.02 (0.16), residues: 1074
  sheet:  0.48 (0.93), residues: 37
  loop : -0.71 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A1495 
 HIS   0.004   0.000   HIS A 729 
 PHE   0.021   0.001   PHE A1605 
 TYR   0.014   0.001   TYR A1260 
 ARG   0.005   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 1.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  589 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6283 (mm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 80
  average time/residue: 1.1962
  time to fit residues: 106.5342
Evaluate side-chains
  75 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  215 GLN
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1128 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 142 optimal weight:   40.0000
   chunk 108 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 144 optimal weight:   10.0000
   chunk 152 optimal weight:    6.9990
   chunk 75 optimal weight:    0.2980
   chunk 136 optimal weight:    0.0070
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.4798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN
A 729 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12977  Z= 0.143
  Angle     :  0.467   7.542  17579  Z= 0.242
  Chirality :  0.036   0.138   2108
  Planarity :  0.003   0.057   2189
  Dihedral  :  3.776  28.103   1656
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.07 %
    Favored  : 88.92 %
  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:  1.89 (0.22), residues: 1569
  helix:  2.08 (0.16), residues: 1086
  sheet:  0.42 (0.93), residues: 37
  loop : -0.77 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A1495 
 HIS   0.003   0.001   HIS A1429 
 PHE   0.020   0.001   PHE A1605 
 TYR   0.013   0.001   TYR A1260 
 ARG   0.004   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 1.485 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5614 (OUTLIER) cc_final: 0.5238 (mt)
REVERT: A 1313 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5854 (mtp85)
  outliers start: 15
  outliers final: 5
  residues processed: 86
  average time/residue: 1.1022
  time to fit residues: 106.0870
Evaluate side-chains
  78 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1152 GLU
Chi-restraints excluded: chain A residue 1313 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 86 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 130 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0370
   chunk 0 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0570
   chunk 137 optimal weight:    0.1980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.3376

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 729 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12977  Z= 0.127
  Angle     :  0.450   7.462  17579  Z= 0.234
  Chirality :  0.036   0.131   2108
  Planarity :  0.003   0.038   2189
  Dihedral  :  3.704  28.124   1656
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.08 %
    Favored  : 88.18 %
  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:  2.03 (0.22), residues: 1569
  helix:  2.20 (0.16), residues: 1091
  sheet:  0.43 (0.94), residues: 37
  loop : -0.77 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1495 
 HIS   0.003   0.001   HIS A1429 
 PHE   0.025   0.001   PHE A 102 
 TYR   0.013   0.001   TYR A1251 
 ARG   0.003   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 1.444 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5224 (mt)
REVERT: A 1313 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5795 (mtp85)
REVERT: A 1374 GLN cc_start: 0.2588 (OUTLIER) cc_final: 0.1690 (tt0)
  outliers start: 11
  outliers final: 3
  residues processed: 85
  average time/residue: 1.1283
  time to fit residues: 107.2342
Evaluate side-chains
  74 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1313 ARG
Chi-restraints excluded: chain A residue 1374 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 137 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 152 optimal weight:   20.0000
   chunk 126 optimal weight:    0.0970
   chunk 70 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
A 360 GLN
A 729 HIS
A1102 GLN
A1153 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12977  Z= 0.152
  Angle     :  0.468   7.245  17579  Z= 0.243
  Chirality :  0.037   0.172   2108
  Planarity :  0.003   0.036   2189
  Dihedral  :  3.721  28.025   1656
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.16 %
    Favored  : 87.04 %
  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:  2.00 (0.22), residues: 1569
  helix:  2.17 (0.16), residues: 1087
  sheet:  0.48 (0.95), residues: 37
  loop : -0.74 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1495 
 HIS   0.003   0.001   HIS A 318 
 PHE   0.020   0.001   PHE A1605 
 TYR   0.016   0.001   TYR A1260 
 ARG   0.007   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.472 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5240 (mt)
REVERT: A 1313 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5859 (mtp85)
REVERT: A 1374 GLN cc_start: 0.2593 (OUTLIER) cc_final: 0.1671 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 81
  average time/residue: 1.1057
  time to fit residues: 101.4303
Evaluate side-chains
  77 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1313 ARG
Chi-restraints excluded: chain A residue 1374 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 128 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 152 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9980
   chunk 92 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0570
   overall best weight:    0.5498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 729 HIS
A1153 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12977  Z= 0.151
  Angle     :  0.467   7.197  17579  Z= 0.243
  Chirality :  0.036   0.138   2108
  Planarity :  0.003   0.036   2189
  Dihedral  :  3.723  27.937   1656
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.63 %
    Favored  : 86.30 %
  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:  2.01 (0.22), residues: 1569
  helix:  2.19 (0.16), residues: 1084
  sheet:  0.48 (0.95), residues: 37
  loop : -0.75 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1495 
 HIS   0.003   0.001   HIS A1429 
 PHE   0.018   0.001   PHE A1605 
 TYR   0.016   0.001   TYR A1260 
 ARG   0.005   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 1.348 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5243 (mt)
REVERT: A 1313 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5920 (mtp85)
REVERT: A 1374 GLN cc_start: 0.2660 (OUTLIER) cc_final: 0.1732 (tt0)
  outliers start: 16
  outliers final: 7
  residues processed: 82
  average time/residue: 1.0649
  time to fit residues: 98.0780
Evaluate side-chains
  77 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1313 ARG
Chi-restraints excluded: chain A residue 1374 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0170
   chunk 29 optimal weight:    0.5980
   chunk 96 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 119 optimal weight:    2.9990
   chunk 138 optimal weight:   10.0000
   overall best weight:    0.8620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 729 HIS
A1153 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12977  Z= 0.195
  Angle     :  0.509   9.163  17579  Z= 0.261
  Chirality :  0.038   0.157   2108
  Planarity :  0.003   0.038   2189
  Dihedral  :  3.810  27.781   1656
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 12.96 %
    Favored  : 86.10 %
  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:  1.85 (0.22), residues: 1569
  helix:  2.06 (0.16), residues: 1083
  sheet:  0.45 (0.95), residues: 37
  loop : -0.78 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1495 
 HIS   0.004   0.001   HIS A 318 
 PHE   0.018   0.001   PHE A1605 
 TYR   0.020   0.001   TYR A1260 
 ARG   0.005   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 1.292 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5260 (mt)
REVERT: A 1313 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5990 (mtp85)
REVERT: A 1358 GLN cc_start: 0.3130 (OUTLIER) cc_final: 0.1635 (tp-100)
REVERT: A 1374 GLN cc_start: 0.2654 (OUTLIER) cc_final: 0.1692 (tt0)
  outliers start: 14
  outliers final: 8
  residues processed: 80
  average time/residue: 1.1111
  time to fit residues: 100.3585
Evaluate side-chains
  79 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1313 ARG
Chi-restraints excluded: chain A residue 1358 GLN
Chi-restraints excluded: chain A residue 1374 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 145 optimal weight:    9.9990
   chunk 133 optimal weight:    1.9990
   chunk 141 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 150 optimal weight:   10.0000
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 729 HIS
A1153 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  12977  Z= 0.266
  Angle     :  0.560   8.655  17579  Z= 0.288
  Chirality :  0.040   0.179   2108
  Planarity :  0.004   0.043   2189
  Dihedral  :  4.017  27.451   1656
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.10 %
    Favored  : 85.83 %
  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:  1.55 (0.22), residues: 1569
  helix:  1.80 (0.16), residues: 1080
  sheet:  0.38 (0.95), residues: 37
  loop : -0.82 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1495 
 HIS   0.005   0.001   HIS A 318 
 PHE   0.018   0.002   PHE A1605 
 TYR   0.025   0.002   TYR A1260 
 ARG   0.006   0.000   ARG A 333 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.347 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5149 (mt)
REVERT: A 1313 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6076 (mtp85)
REVERT: A 1374 GLN cc_start: 0.2694 (OUTLIER) cc_final: 0.1752 (tt0)
  outliers start: 16
  outliers final: 7
  residues processed: 83
  average time/residue: 1.0693
  time to fit residues: 100.6173
Evaluate side-chains
  80 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1313 ARG
Chi-restraints excluded: chain A residue 1374 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 157 optimal weight:    9.9990
   chunk 144 optimal weight:    4.9990
   chunk 125 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0170
   chunk 133 optimal weight:    2.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 729 HIS
A1093 ASN
A1151 ASN
A1153 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  12977  Z= 0.156
  Angle     :  0.500   8.927  17579  Z= 0.258
  Chirality :  0.037   0.148   2108
  Planarity :  0.003   0.041   2189
  Dihedral  :  3.846  27.618   1656
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 13.57 %
    Favored  : 85.83 %
  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:  1.83 (0.22), residues: 1569
  helix:  2.05 (0.16), residues: 1079
  sheet:  0.41 (0.96), residues: 37
  loop : -0.80 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1495 
 HIS   0.003   0.001   HIS A1429 
 PHE   0.018   0.001   PHE A1605 
 TYR   0.013   0.001   TYR A1251 
 ARG   0.005   0.000   ARG A 333 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 1.531 
Fit side-chains
REVERT: A 1053 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.5306 (mt)
REVERT: A 1313 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6010 (mtp85)
REVERT: A 1374 GLN cc_start: 0.2645 (OUTLIER) cc_final: 0.1732 (tt0)
  outliers start: 9
  outliers final: 5
  residues processed: 78
  average time/residue: 1.0048
  time to fit residues: 89.1564
Evaluate side-chains
  73 residues out of total 1489 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1313 ARG
Chi-restraints excluded: chain A residue 1374 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 115 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0670
   chunk 125 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 110 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 729 HIS
A1153 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.230463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.192443 restraints weight = 13002.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.4191 rms_B_bonded: 1.21
r_work: 0.3800 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061  12977  Z= 0.159
  Angle     :  0.501   8.820  17579  Z= 0.258
  Chirality :  0.037   0.135   2108
  Planarity :  0.003   0.038   2189
  Dihedral  :  3.790  27.745   1656
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 13.83 %
    Favored  : 85.43 %
  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:  1.89 (0.22), residues: 1569
  helix:  2.09 (0.16), residues: 1082
  sheet:  0.43 (0.95), residues: 37
  loop : -0.76 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1495 
 HIS   0.003   0.001   HIS A 318 
 PHE   0.025   0.001   PHE A 102 
 TYR   0.013   0.001   TYR A1251 
 ARG   0.008   0.000   ARG A 333 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3845.04 seconds
wall clock time: 69 minutes 50.04 seconds (4190.04 seconds total)