Starting phenix.real_space_refine
on Tue Sep 24 18:35:04 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/09_2024/7pq5_13587.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/09_2024/7pq5_13587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/09_2024/7pq5_13587.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/09_2024/7pq5_13587.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/09_2024/7pq5_13587.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/09_2024/7pq5_13587.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      16      5.16       5
     C    5317      2.51       5
     N    1557      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8512
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "L"
      Number of atoms: 8512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1047, 8512
          Classifications: {'peptide': 1047}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 48, 'TRANS': 998}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 5.11, per 1000 atoms: 0.60
  Number of scatterers: 8512
  At special positions: 0
  Unit cell: (84.63, 98.58, 122.76, 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      16     16.00
     O    1622      8.00
     N    1557      7.00
     C    5317      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: 1.95
  Conformation dependent library (CDL) restraints added in 914.4 milliseconds
  

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 8 sheets defined
      1.1% alpha, 39.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'L' and resid 530 through 532
      No H-bonds generated for 'chain 'L' and resid 530 through 532'
    Processing helix  chain 'L' and resid 646 through 648
      No H-bonds generated for 'chain 'L' and resid 646 through 648'
    Processing helix  chain 'L' and resid 1277 through 1281
    Processing sheet with id=AA1, first strand: chain 'L' and resid 300 through 306
      removed outlier: 6.600A  pdb=" N   PHE L 314 " --> pdb=" O   ASP L 303 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR L 305 " --> pdb=" O   LEU L 312 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU L 312 " --> pdb=" O   THR L 305 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLY L 329 " --> pdb=" O   VAL L 319 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   GLU L 321 " --> pdb=" O   GLY L 327 " (cutoff:3.500A)
      removed outlier: 11.547A  pdb=" N   GLY L 327 " --> pdb=" O   GLU L 321 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 354 through 358
      removed outlier: 4.150A  pdb=" N   CYS L 337 " --> pdb=" O   ARG L 348 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU L 398 " --> pdb=" O   LEU L 413 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 365 through 366
      removed outlier: 4.633A  pdb=" N   HIS L 387 " --> pdb=" O   VAL L 392 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   VAL L 392 " --> pdb=" O   HIS L 387 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU L 416 " --> pdb=" O   TYR L 395 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   THR L 436 " --> pdb=" O   LEU L 448 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU L 458 " --> pdb=" O   LEU L 449 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   THR L 457 " --> pdb=" O   ARG L 472 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ARG L 472 " --> pdb=" O   THR L 457 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ILE L 459 " --> pdb=" O   MET L 470 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   HIS L 474 " --> pdb=" O   GLU L 483 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   ALA L 482 " --> pdb=" O   TYR L 494 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TYR L 493 " --> pdb=" O   TRP L 505 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   TRP L 505 " --> pdb=" O   TYR L 493 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLU L 495 " --> pdb=" O   SER L 503 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   SER L 503 " --> pdb=" O   TYR L 515 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TRP L 505 " --> pdb=" O   VAL L 513 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP L 525 " --> pdb=" O   ARG L 516 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   THR L 524 " --> pdb=" O   LEU L 537 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR L 544 " --> pdb=" O   GLY L 556 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   THR L 555 " --> pdb=" O   ILE L 567 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ILE L 567 " --> pdb=" O   THR L 555 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   HIS L 557 " --> pdb=" O   THR L 565 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   THR L 565 " --> pdb=" O   TYR L 577 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   VAL L 586 " --> pdb=" O   LEU L 598 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER L 609 " --> pdb=" O   THR L 599 " (cutoff:3.500A)
      removed outlier: 5.445A  pdb=" N   THR L 608 " --> pdb=" O   TYR L 620 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   THR L 630 " --> pdb=" O   PRO L 642 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLY L 652 " --> pdb=" O   GLN L 643 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ALA L 651 " --> pdb=" O   LEU L 663 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU L 663 " --> pdb=" O   ALA L 651 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER L 673 " --> pdb=" O   THR L 664 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   THR L 672 " --> pdb=" O   GLN L 684 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG L 694 " --> pdb=" O   GLU L 685 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   VAL L 693 " --> pdb=" O   LEU L 705 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ARG L 714 " --> pdb=" O   TRP L 725 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ARG L 724 " --> pdb=" O   SER L 736 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   SER L 736 " --> pdb=" O   ARG L 724 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ARG L 726 " --> pdb=" O   ALA L 734 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   ALA L 734 " --> pdb=" O   PHE L 746 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   THR L 755 " --> pdb=" O   VAL L 767 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA L 777 " --> pdb=" O   GLU L 768 " (cutoff:3.500A)
      removed outlier: 5.488A  pdb=" N   VAL L 776 " --> pdb=" O   TYR L 788 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   GLN L 787 " --> pdb=" O   VAL L 800 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   VAL L 800 " --> pdb=" O   GLN L 787 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ARG L 789 " --> pdb=" O   THR L 798 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   THR L 798 " --> pdb=" O   TYR L 810 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR L 820 " --> pdb=" O   THR L 811 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ILE L 819 " --> pdb=" O   TYR L 831 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU L 841 " --> pdb=" O   ARG L 832 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ILE L 840 " --> pdb=" O   TYR L 852 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   THR L 861 " --> pdb=" O   TYR L 872 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR L 882 " --> pdb=" O   HIS L 873 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU L 881 " --> pdb=" O   PHE L 892 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER L 888 " --> pdb=" O   SER L 885 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   THR L 889 " --> pdb=" O   GLN L 905 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   GLN L 905 " --> pdb=" O   THR L 889 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   HIS L 891 " --> pdb=" O   GLU L 903 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLU L 903 " --> pdb=" O   HIS L 891 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   GLU L 893 " --> pdb=" O   VAL L 901 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ARG L 899 " --> pdb=" O   ASP L 895 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   VAL L 901 " --> pdb=" O   ARG L 912 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY L 908 " --> pdb=" O   GLN L 905 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR L 961 " --> pdb=" O   GLU L 952 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   ILE L 960 " --> pdb=" O   ILE L 972 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY L 982 " --> pdb=" O   GLU L 973 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   THR L 981 " --> pdb=" O   GLN L 993 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA L1003 " --> pdb=" O   GLN L 994 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   THR L1002 " --> pdb=" O   TYR L1033 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   THR L1042 " --> pdb=" O   TYR L1053 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP L1046 " --> pdb=" O   GLN L1049 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER L1063 " --> pdb=" O   LEU L1054 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   GLU L1066 " --> pdb=" O   LEU L1070 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   LEU L1070 " --> pdb=" O   GLU L1066 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 1086 through 1087
    Processing sheet with id=AA5, first strand: chain 'L' and resid 1098 through 1099
      removed outlier: 3.720A  pdb=" N   ARG L1103 " --> pdb=" O   GLN L1099 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 1106 through 1107
      removed outlier: 6.066A  pdb=" N   GLN L1121 " --> pdb=" O   TYR L1137 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG L1159 " --> pdb=" O   GLU L1168 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   THR L1167 " --> pdb=" O   TYR L1180 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   ALA L1188 " --> pdb=" O   HIS L1203 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   HIS L1203 " --> pdb=" O   ALA L1188 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE L1190 " --> pdb=" O   ILE L1201 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ILE L1201 " --> pdb=" O   ILE L1190 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   GLU L1192 " --> pdb=" O   LYS L1199 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL L1212 " --> pdb=" O   ALA L1239 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   TYR L1238 " --> pdb=" O   LEU L1250 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LEU L1250 " --> pdb=" O   TYR L1238 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL L1240 " --> pdb=" O   LEU L1248 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   LEU L1248 " --> pdb=" O   ARG L1260 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ARG L1260 " --> pdb=" O   LEU L1248 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU L1250 " --> pdb=" O   VAL L1258 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 1290 through 1291
      removed outlier: 3.500A  pdb=" N   CYS L1311 " --> pdb=" O   LEU L1306 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 1336 through 1337

    272 hydrogen bonds defined for protein.
    753 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: 4.51

  Time building geometry restraints manager: 2.30 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: 2924
        1.34 -     1.46: 1753
        1.46 -     1.58: 4029
        1.58 -     1.69: 0
        1.69 -     1.81: 23
  Bond restraints: 8729
  Sorted by residual:
  bond pdb=" N   ALA L 602 "
       pdb=" CA  ALA L 602 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.021 1.29e-02 6.01e+03 2.59e+00
  bond pdb=" CA  ASP L 509 "
       pdb=" C   ASP L 509 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.34e-02 5.57e+03 1.11e+00
  bond pdb=" N   SER L1083 "
       pdb=" CA  SER L1083 "
    ideal  model  delta    sigma   weight residual
    1.459  1.446  0.013 1.22e-02 6.72e+03 1.07e+00
  bond pdb=" CA  ASP L 509 "
       pdb=" CB  ASP L 509 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 1.00e+00
  bond pdb=" CA  PHE L1086 "
       pdb=" CB  PHE L1086 "
    ideal  model  delta    sigma   weight residual
    1.535  1.555 -0.020 2.09e-02 2.29e+03 9.16e-01
  ... (remaining 8724 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11593
        2.38 -     4.75: 230
        4.75 -     7.13: 26
        7.13 -     9.51: 6
        9.51 -    11.89: 2
  Bond angle restraints: 11857
  Sorted by residual:
  angle pdb=" N   LEU L 601 "
        pdb=" CA  LEU L 601 "
        pdb=" C   LEU L 601 "
      ideal   model   delta    sigma   weight residual
     108.41   98.53    9.88 1.61e+00 3.86e-01 3.77e+01
  angle pdb=" C   ALA L 602 "
        pdb=" N   ASP L 603 "
        pdb=" CA  ASP L 603 "
      ideal   model   delta    sigma   weight residual
     122.60  113.15    9.45 1.56e+00 4.11e-01 3.67e+01
  angle pdb=" N   ARG L1084 "
        pdb=" CA  ARG L1084 "
        pdb=" C   ARG L1084 "
      ideal   model   delta    sigma   weight residual
     110.80   98.91   11.89 2.13e+00 2.20e-01 3.11e+01
  angle pdb=" C   LEU L 601 "
        pdb=" N   ALA L 602 "
        pdb=" CA  ALA L 602 "
      ideal   model   delta    sigma   weight residual
     121.54  130.05   -8.51 1.91e+00 2.74e-01 1.98e+01
  angle pdb=" CA  PHE L1086 "
        pdb=" CB  PHE L1086 "
        pdb=" CG  PHE L1086 "
      ideal   model   delta    sigma   weight residual
     113.80  117.09   -3.29 1.00e+00 1.00e+00 1.08e+01
  ... (remaining 11852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4621
       17.82 -    35.64: 348
       35.64 -    53.46: 92
       53.46 -    71.28: 30
       71.28 -    89.10: 20
  Dihedral angle restraints: 5111
    sinusoidal: 2106
      harmonic: 3005
  Sorted by residual:
  dihedral pdb=" CA  ASP L 422 "
           pdb=" C   ASP L 422 "
           pdb=" N   ASN L 423 "
           pdb=" CA  ASN L 423 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.75   26.25     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ALA L1355 "
           pdb=" C   ALA L1355 "
           pdb=" N   GLY L1356 "
           pdb=" CA  GLY L1356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.76  -25.24     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  GLY L 556 "
           pdb=" C   GLY L 556 "
           pdb=" N   HIS L 557 "
           pdb=" CA  HIS L 557 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.30   24.70     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 5108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 886
       0.052 -    0.105: 259
       0.105 -    0.157: 74
       0.157 -    0.210: 2
       0.210 -    0.262: 1
  Chirality restraints: 1222
  Sorted by residual:
  chirality pdb=" CA  PHE L1086 "
            pdb=" N   PHE L1086 "
            pdb=" C   PHE L1086 "
            pdb=" CB  PHE L1086 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  HIS L 907 "
            pdb=" N   HIS L 907 "
            pdb=" C   HIS L 907 "
            pdb=" CB  HIS L 907 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.98e-01
  chirality pdb=" CA  HIS L1102 "
            pdb=" N   HIS L1102 "
            pdb=" C   HIS L1102 "
            pdb=" CB  HIS L1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.59e-01
  ... (remaining 1219 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L1081 "    0.059 5.00e-02 4.00e+02   8.77e-02 1.23e+01
        pdb=" N   PRO L1082 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO L1082 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO L1082 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 832 "    0.078 9.50e-02 1.11e+02   4.58e-02 1.17e+01
        pdb=" NE  ARG L 832 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 832 "    0.056 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 832 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 832 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE L1086 "   -0.029 2.00e-02 2.50e+03   2.41e-02 1.02e+01
        pdb=" CG  PHE L1086 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE L1086 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE L1086 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE L1086 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE L1086 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE L1086 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1687
        2.78 -     3.31: 6655
        3.31 -     3.84: 12598
        3.84 -     4.37: 15803
        4.37 -     4.90: 28761
  Nonbonded interactions: 65504
  Sorted by model distance:
  nonbonded pdb=" O   LEU L 456 "
            pdb=" OH  TYR L 475 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OD1 ASP L 916 "
            pdb=" N   ASN L 917 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OG1 THR L 511 "
            pdb=" O   PRO L 771 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OD1 ASP L 509 "
            pdb=" N   GLN L 510 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OD1 ASP L 645 "
            pdb=" N   GLU L 646 "
     model   vdw
     2.344 3.120
  ... (remaining 65499 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.410
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
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   0.039   8729  Z= 0.305
  Angle     :  0.852  11.886  11857  Z= 0.491
  Chirality :  0.052   0.262   1222
  Planarity :  0.006   0.088   1580
  Dihedral  : 15.553  89.105   3213
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.53 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  6.98 %
    Favored  : 90.20 %
  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: -0.13 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.40 (0.28), residues: 327
  loop : -0.88 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP L 505 
 HIS   0.006   0.001   HIS L1203 
 PHE   0.055   0.003   PHE L1086 
 TYR   0.021   0.003   TYR L 533 
 ARG   0.057   0.005   ARG L 832 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  411 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7627 (ttm110)
REVERT: L  835 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8164 (mtt90)
REVERT: L  885 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8788 (p)
REVERT: L 1152 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.5662 (m-30)
  outliers start: 25
  outliers final: 11
  residues processed: 106
  average time/residue: 0.3183
  time to fit residues: 42.6400
Evaluate side-chains
  61 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  276 ARG
Chi-restraints excluded: chain L residue  377 SER
Chi-restraints excluded: chain L residue  411 ARG
Chi-restraints excluded: chain L residue  509 ASP
Chi-restraints excluded: chain L residue  569 THR
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue  876 SER
Chi-restraints excluded: chain L residue  885 SER
Chi-restraints excluded: chain L residue  925 LEU
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1097 LEU
Chi-restraints excluded: chain L residue 1152 ASP
Chi-restraints excluded: chain L residue 1183 ASP
Chi-restraints excluded: chain L residue 1320 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.0050
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   overall best weight:    1.4998

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

Flipped N/Q/H residues before XYZ refinement:
L 368 ASN
L 371 HIS
L 387 HIS
L 455 GLN
L 488 GLN
L 680 ASN
L 848 ASN
L 897 GLN
L 923 GLN
L 967 GLN
L1058 ASN
L1110 HIS
L1195 HIS
L1225 ASN
L1289 GLN
L1300 ASN
L1325 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8729  Z= 0.270
  Angle     :  0.668   8.573  11857  Z= 0.363
  Chirality :  0.046   0.167   1222
  Planarity :  0.005   0.051   1580
  Dihedral  :  7.359  59.057   1233
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.57 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.44 (0.27), residues: 341
  loop : -0.56 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L 505 
 HIS   0.003   0.001   HIS L 891 
 PHE   0.028   0.002   PHE L1086 
 TYR   0.017   0.001   TYR L1193 
 ARG   0.005   0.000   ARG L1008 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  885 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8717 (p)
REVERT: L 1152 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5141 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 72
  average time/residue: 0.2871
  time to fit residues: 27.0946
Evaluate side-chains
  54 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  419 ASP
Chi-restraints excluded: chain L residue  569 THR
Chi-restraints excluded: chain L residue  581 ARG
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue  885 SER
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1097 LEU
Chi-restraints excluded: chain L residue 1145 LEU
Chi-restraints excluded: chain L residue 1152 ASP
Chi-restraints excluded: chain L residue 1183 ASP
Chi-restraints excluded: chain L residue 1320 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 78 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
L 400 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   8729  Z= 0.256
  Angle     :  0.595   6.734  11857  Z= 0.322
  Chirality :  0.045   0.153   1222
  Planarity :  0.005   0.050   1580
  Dihedral  :  6.390  55.902   1219
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.35 %
    Favored  : 88.63 %
  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:  0.14 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.22 (0.27), residues: 359
  loop : -0.57 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 723 
 HIS   0.003   0.001   HIS L 864 
 PHE   0.024   0.001   PHE L1086 
 TYR   0.014   0.001   TYR L1193 
 ARG   0.002   0.000   ARG L 465 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: L  885 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8632 (p)
REVERT: L 1142 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: L 1152 ASP cc_start: 0.6247 (OUTLIER) cc_final: 0.4786 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 68
  average time/residue: 0.2954
  time to fit residues: 27.3125
Evaluate side-chains
  58 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  419 ASP
Chi-restraints excluded: chain L residue  569 THR
Chi-restraints excluded: chain L residue  581 ARG
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue  885 SER
Chi-restraints excluded: chain L residue 1070 LEU
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1097 LEU
Chi-restraints excluded: chain L residue 1145 LEU
Chi-restraints excluded: chain L residue 1152 ASP
Chi-restraints excluded: chain L residue 1320 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
L 923 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   8729  Z= 0.480
  Angle     :  0.688   9.356  11857  Z= 0.372
  Chirality :  0.048   0.165   1222
  Planarity :  0.005   0.052   1580
  Dihedral  :  6.356  54.661   1217
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  9.80 %
    Favored  : 87.39 %
  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: -0.10 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.13 (0.27), residues: 357
  loop : -0.77 (0.22), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 723 
 HIS   0.005   0.001   HIS L 751 
 PHE   0.034   0.002   PHE L1086 
 TYR   0.017   0.002   TYR L 533 
 ARG   0.007   0.000   ARG L 946 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 42
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: L 1069 THR cc_start: 0.8310 (m) cc_final: 0.7989 (p)
REVERT: L 1142 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: L 1152 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.5341 (m-30)
  outliers start: 25
  outliers final: 13
  residues processed: 62
  average time/residue: 0.2127
  time to fit residues: 18.9417
Evaluate side-chains
  56 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  415 THR
Chi-restraints excluded: chain L residue  419 ASP
Chi-restraints excluded: chain L residue  432 HIS
Chi-restraints excluded: chain L residue  502 ILE
Chi-restraints excluded: chain L residue  546 SER
Chi-restraints excluded: chain L residue  569 THR
Chi-restraints excluded: chain L residue  581 ARG
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue  767 VAL
Chi-restraints excluded: chain L residue 1149 ILE
Chi-restraints excluded: chain L residue 1152 ASP
Chi-restraints excluded: chain L residue 1154 ILE
Chi-restraints excluded: chain L residue 1308 GLU
Chi-restraints excluded: chain L residue 1320 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
L 948 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8729  Z= 0.272
  Angle     :  0.587   7.186  11857  Z= 0.317
  Chirality :  0.044   0.153   1222
  Planarity :  0.005   0.053   1580
  Dihedral  :  5.728  52.737   1213
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.70 %
    Favored  : 87.27 %
  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: -0.19 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.02 (0.27), residues: 346
  loop : -0.77 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 505 
 HIS   0.003   0.001   HIS L1102 
 PHE   0.027   0.001   PHE L1086 
 TYR   0.013   0.001   TYR L1193 
 ARG   0.005   0.000   ARG L1084 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: L 1069 THR cc_start: 0.8279 (m) cc_final: 0.7953 (p)
REVERT: L 1142 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: L 1189 GLU cc_start: 0.7596 (tt0) cc_final: 0.7377 (tt0)
  outliers start: 18
  outliers final: 14
  residues processed: 60
  average time/residue: 0.2299
  time to fit residues: 19.4130
Evaluate side-chains
  57 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  415 THR
Chi-restraints excluded: chain L residue  419 ASP
Chi-restraints excluded: chain L residue  432 HIS
Chi-restraints excluded: chain L residue  569 THR
Chi-restraints excluded: chain L residue  581 ARG
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue  767 VAL
Chi-restraints excluded: chain L residue  901 VAL
Chi-restraints excluded: chain L residue 1070 LEU
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1149 ILE
Chi-restraints excluded: chain L residue 1152 ASP
Chi-restraints excluded: chain L residue 1308 GLU
Chi-restraints excluded: chain L residue 1320 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 59 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0670
   chunk 83 optimal weight:    0.0970
   chunk 46 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0970
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.2914

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

Flipped N/Q/H residues before XYZ refinement:
L 568 HIS
L 748 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8729  Z= 0.111
  Angle     :  0.503   5.439  11857  Z= 0.270
  Chirality :  0.042   0.137   1222
  Planarity :  0.004   0.054   1580
  Dihedral  :  5.044  49.482   1213
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 12.16 %
    Favored  : 86.94 %
  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: -0.01 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.13 (0.27), residues: 359
  loop : -0.68 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 505 
 HIS   0.002   0.000   HIS L 476 
 PHE   0.018   0.001   PHE L1086 
 TYR   0.008   0.001   TYR L 984 
 ARG   0.006   0.000   ARG L 946 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L 1229 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.5245 (mp)
  outliers start: 8
  outliers final: 2
  residues processed: 61
  average time/residue: 0.2797
  time to fit residues: 22.8892
Evaluate side-chains
  47 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1152 ASP
Chi-restraints excluded: chain L residue 1229 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
L 365 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8729  Z= 0.151
  Angle     :  0.526   7.960  11857  Z= 0.284
  Chirality :  0.042   0.144   1222
  Planarity :  0.004   0.054   1580
  Dihedral  :  4.672  48.409   1209
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.05 %
    Favored  : 86.94 %
  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:  0.05 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.25 (0.27), residues: 358
  loop : -0.68 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 505 
 HIS   0.007   0.001   HIS L 365 
 PHE   0.020   0.001   PHE L1086 
 TYR   0.010   0.001   TYR L 984 
 ARG   0.007   0.000   ARG L 946 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: L 1100 GLU cc_start: 0.7279 (tp30) cc_final: 0.7076 (tp30)
REVERT: L 1152 ASP cc_start: 0.6316 (OUTLIER) cc_final: 0.5663 (p0)
  outliers start: 9
  outliers final: 3
  residues processed: 55
  average time/residue: 0.2529
  time to fit residues: 18.9751
Evaluate side-chains
  50 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  432 HIS
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1145 LEU
Chi-restraints excluded: chain L residue 1152 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 91 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   8729  Z= 0.271
  Angle     :  0.590   9.707  11857  Z= 0.317
  Chirality :  0.044   0.154   1222
  Planarity :  0.005   0.054   1580
  Dihedral  :  4.889  46.832   1209
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.94 %
    Favored  : 87.16 %
  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: -0.04 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.18 (0.27), residues: 359
  loop : -0.75 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 829 
 HIS   0.005   0.001   HIS L 748 
 PHE   0.025   0.001   PHE L1086 
 TYR   0.011   0.001   TYR L 984 
 ARG   0.007   0.000   ARG L 946 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: L 1230 MET cc_start: 0.6315 (ttt) cc_final: 0.5841 (ttp)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 0.2509
  time to fit residues: 17.8313
Evaluate side-chains
  47 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  432 HIS
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1149 ILE
Chi-restraints excluded: chain L residue 1152 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0020
   chunk 88 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.7590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8729  Z= 0.161
  Angle     :  0.549   8.946  11857  Z= 0.296
  Chirality :  0.042   0.144   1222
  Planarity :  0.004   0.054   1580
  Dihedral  :  4.710  49.531   1209
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.61 %
    Favored  : 86.71 %
  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: -0.00 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.23 (0.27), residues: 359
  loop : -0.73 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 505 
 HIS   0.003   0.001   HIS L 748 
 PHE   0.021   0.001   PHE L1086 
 TYR   0.010   0.001   TYR L 984 
 ARG   0.008   0.000   ARG L 946 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: L 1100 GLU cc_start: 0.7220 (tp30) cc_final: 0.6997 (tp30)
REVERT: L 1230 MET cc_start: 0.6034 (ttt) cc_final: 0.5638 (ttp)
  outliers start: 6
  outliers final: 6
  residues processed: 50
  average time/residue: 0.2719
  time to fit residues: 18.7207
Evaluate side-chains
  49 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  432 HIS
Chi-restraints excluded: chain L residue  546 SER
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1149 ILE
Chi-restraints excluded: chain L residue 1152 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0970
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.5784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8729  Z= 0.270
  Angle     :  0.583   9.270  11857  Z= 0.314
  Chirality :  0.044   0.152   1222
  Planarity :  0.005   0.054   1580
  Dihedral  :  4.898  48.328   1209
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.84 %
    Favored  : 86.49 %
  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: -0.07 (0.25), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.17 (0.27), residues: 358
  loop : -0.77 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 829 
 HIS   0.005   0.001   HIS L 748 
 PHE   0.024   0.001   PHE L1086 
 TYR   0.011   0.001   TYR L 984 
 ARG   0.008   0.000   ARG L 946 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: L 1100 GLU cc_start: 0.7239 (tp30) cc_final: 0.6996 (tp30)
REVERT: L 1230 MET cc_start: 0.6047 (ttt) cc_final: 0.5704 (ttp)
  outliers start: 6
  outliers final: 6
  residues processed: 47
  average time/residue: 0.2681
  time to fit residues: 17.5312
Evaluate side-chains
  48 residues out of total 890 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  432 HIS
Chi-restraints excluded: chain L residue  546 SER
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue 1089 VAL
Chi-restraints excluded: chain L residue 1149 ILE
Chi-restraints excluded: chain L residue 1152 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0970
   overall best weight:    0.6778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.094254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.078060 restraints weight = 15266.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.21
r_work: 0.2831 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8729  Z= 0.153
  Angle     :  0.539   8.911  11857  Z= 0.290
  Chirality :  0.042   0.143   1222
  Planarity :  0.004   0.054   1580
  Dihedral  :  4.680  51.063   1209
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.84 %
    Favored  : 86.49 %
  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: -0.02 (0.26), residues: 1037
  helix:  None (None), residues: 0
  sheet:  1.23 (0.27), residues: 359
  loop : -0.75 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 505 
 HIS   0.003   0.001   HIS L 748 
 PHE   0.020   0.001   PHE L1086 
 TYR   0.010   0.001   TYR L 984 
 ARG   0.008   0.000   ARG L 946 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1815.63 seconds
wall clock time: 32 minutes 54.29 seconds (1974.29 seconds total)