Starting phenix.real_space_refine
on Sat Dec  9 15:44:03 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/12_2023/8qa5_18299_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/12_2023/8qa5_18299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/12_2023/8qa5_18299.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/12_2023/8qa5_18299.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/12_2023/8qa5_18299_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/12_2023/8qa5_18299_trim_updated.pdb"
  }
  resolution = 3.14
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1148 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      10      5.16       5
     C    3426      2.51       5
     N    1013      2.21       5
     O    1116      1.98       5
     H    4771      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  344": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  358": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  377": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  476": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  535": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B GLU  458": "OE1" <-> "OE2"
    Residue "B ARG  473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  476": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B PHE  515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  535": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 10338
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 6547
          Classifications: {'peptide': 582}
          Link IDs: {'PTRANS': 35, 'TRANS': 546}
          Chain breaks: 3
          Unresolved chain link angles: 14
          Unresolved non-hydrogen bonds: 1173
          Unresolved non-hydrogen angles: 1685
          Unresolved non-hydrogen dihedrals: 765
          Unresolved non-hydrogen chiralities: 342
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 10, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 16, 'GLU:plan': 22, 'ARG:plan': 18}
          Unresolved non-hydrogen planarities: 554
    Chain: "B"
      Number of atoms: 3686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3686
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 14, 'TRANS': 215}
    Chain: "A"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 79
          Unusual residues: {'FAD': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 5.39, per 1000 atoms: 0.52
  Number of scatterers: 10338
  At special positions: 0
  Unit cell: (106.19, 114.8, 76.916, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      10     16.00
     P       2     15.00
     O    1116      8.00
     N    1013      7.00
     C    3426      6.00
     H    4771      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 8.77
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  996

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      31 helices and 5 sheets defined
      39.6% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 70 through 86
      removed outlier: 4.147A  pdb=" N   ALA A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLY A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 117
    Processing helix  chain 'A' and resid 135 through 147
    Processing helix  chain 'A' and resid 175 through 186
    Processing helix  chain 'A' and resid 207 through 221
      removed outlier: 3.673A  pdb=" N   GLY A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 245
    Processing helix  chain 'A' and resid 262 through 272
      removed outlier: 4.004A  pdb=" N   ARG A 266 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 287
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 291 through 311
    Processing helix  chain 'A' and resid 327 through 335
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 4.620A  pdb=" N   SER A 369 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 378
    Processing helix  chain 'A' and resid 417 through 421
      removed outlier: 3.515A  pdb=" N   TRP A 421 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 440
      removed outlier: 3.869A  pdb=" N   GLU A 433 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 465
    Processing helix  chain 'A' and resid 469 through 477
      removed outlier: 4.229A  pdb=" N   GLN A 477 " --> pdb=" O   ARG A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 531
      removed outlier: 4.692A  pdb=" N   LYS A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   LYS A 531 " --> pdb=" O   GLN A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 554
      No H-bonds generated for 'chain 'A' and resid 552 through 554'
    Processing helix  chain 'A' and resid 579 through 592
      removed outlier: 4.100A  pdb=" N   ASP A 585 " --> pdb=" O   MET A 581 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLU A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   TRP A 591 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ILE A 592 " --> pdb=" O   PHE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
    Processing helix  chain 'A' and resid 636 through 643
      removed outlier: 4.064A  pdb=" N   LEU A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU A 643 " --> pdb=" O   THR A 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 421
      No H-bonds generated for 'chain 'B' and resid 418 through 421'
    Processing helix  chain 'B' and resid 428 through 439
      removed outlier: 3.851A  pdb=" N   VAL B 434 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE B 435 " --> pdb=" O   VAL B 431 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 466
    Processing helix  chain 'B' and resid 468 through 477
    Processing helix  chain 'B' and resid 519 through 532
      removed outlier: 4.064A  pdb=" N   GLU B 523 " --> pdb=" O   ARG B 519 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA B 524 " --> pdb=" O   GLU B 520 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   LYS B 531 " --> pdb=" O   GLN B 527 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR B 532 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 593
      removed outlier: 4.399A  pdb=" N   ASP B 585 " --> pdb=" O   MET B 581 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLU B 586 " --> pdb=" O   PHE B 582 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA B 589 " --> pdb=" O   ASP B 585 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   TRP B 591 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ILE B 592 " --> pdb=" O   PHE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 598
      No H-bonds generated for 'chain 'B' and resid 596 through 598'
    Processing helix  chain 'B' and resid 604 through 613
    Processing helix  chain 'B' and resid 632 through 643
    Processing sheet with id=  A, first strand: chain 'A' and resid 224 through 226
      removed outlier: 3.502A  pdb=" N   PHE A 224 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS A 193 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ALA A 195 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ASN A 152 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ILE A  91 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   HIS A 127 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   VAL A  93 " --> pdb=" O   HIS A 127 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   THR A 129 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 9.313A  pdb=" N   ASP A  92 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   LEU A  62 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   TYR A 321 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ILE A 256 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 506 through 509
    Processing sheet with id=  C, first strand: chain 'A' and resid 547 through 550
      removed outlier: 3.914A  pdb=" N   ALA A 511 " --> pdb=" O   ASP A 623 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN A 483 " --> pdb=" O   GLU A 514 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   PHE A 516 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   THR A 481 " --> pdb=" O   PHE A 516 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 506 through 509
      removed outlier: 6.654A  pdb=" N   THR B 573 " --> pdb=" O   VAL B 559 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 546 through 549
      removed outlier: 4.018A  pdb=" N   GLU B 546 " --> pdb=" O   ASN B 542 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN B 542 " --> pdb=" O   GLU B 546 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ALA B 511 " --> pdb=" O   ASP B 623 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   PHE B 516 " --> pdb=" O   THR B 481 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   THR B 481 " --> pdb=" O   PHE B 516 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   SER B 518 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   ILE B 479 " --> pdb=" O   SER B 518 " (cutoff:3.500A)

    237 hydrogen bonds defined for protein.
    660 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.60

  Time building geometry restraints manager: 9.07 seconds

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

  Histogram of bond lengths:
        0.85 -     1.05: 1424
        1.05 -     1.24: 4190
        1.24 -     1.43: 1785
        1.43 -     1.62: 3056
        1.62 -     1.82: 16
  Bond restraints: 10471
  Sorted by residual:
  bond pdb=" CZ  ARG B 473 "
       pdb=" NH2 ARG B 473 "
    ideal  model  delta    sigma   weight residual
    1.330  1.231  0.099 1.30e-02 5.92e+03 5.81e+01
  bond pdb=" N   SER B 503 "
       pdb=" H   SER B 503 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   LEU B 418 "
       pdb=" H   LEU B 418 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ALA A 353 "
       pdb=" H   ALA A 353 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CE1 PHE A 366 "
       pdb=" HE1 PHE A 366 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  ... (remaining 10466 not shown)

  Histogram of bond angle deviations from ideal:
       96.01 -   104.13: 161
      104.13 -   112.24: 10062
      112.24 -   120.36: 5089
      120.36 -   128.48: 3006
      128.48 -   136.60: 74
  Bond angle restraints: 18392
  Sorted by residual:
  angle pdb=" CA  ASP B 495 "
        pdb=" CB  ASP B 495 "
        pdb=" CG  ASP B 495 "
      ideal   model   delta    sigma   weight residual
     112.60  119.69   -7.09 1.00e+00 1.00e+00 5.03e+01
  angle pdb=" CA  ASN B 644 "
        pdb=" CB  ASN B 644 "
        pdb=" CG  ASN B 644 "
      ideal   model   delta    sigma   weight residual
     112.60  118.32   -5.72 1.00e+00 1.00e+00 3.27e+01
  angle pdb=" CA  PHE B 432 "
        pdb=" CB  PHE B 432 "
        pdb=" CG  PHE B 432 "
      ideal   model   delta    sigma   weight residual
     113.80  119.42   -5.62 1.00e+00 1.00e+00 3.16e+01
  angle pdb=" N   SER A 603 "
        pdb=" CA  SER A 603 "
        pdb=" CB  SER A 603 "
      ideal   model   delta    sigma   weight residual
     111.27  106.05    5.22 9.40e-01 1.13e+00 3.08e+01
  angle pdb=" C   PRO A 413 "
        pdb=" N   LYS A 414 "
        pdb=" CA  LYS A 414 "
      ideal   model   delta    sigma   weight residual
     120.38  128.36   -7.98 1.46e+00 4.69e-01 2.99e+01
  ... (remaining 18387 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.20: 4269
       25.20 -    50.40: 175
       50.40 -    75.60: 64
       75.60 -   100.81: 6
      100.81 -   126.01: 1
  Dihedral angle restraints: 4515
    sinusoidal: 2336
      harmonic: 2179
  Sorted by residual:
  dihedral pdb=" CA  GLU A 458 "
           pdb=" C   GLU A 458 "
           pdb=" N   PRO A 459 "
           pdb=" CA  PRO A 459 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.02   28.98     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  LEU A 405 "
           pdb=" C   LEU A 405 "
           pdb=" N   PHE A 406 "
           pdb=" CA  PHE A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.49  -28.51     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  ILE B 482 "
           pdb=" C   ILE B 482 "
           pdb=" N   ASN B 483 "
           pdb=" CA  ASN B 483 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.67   28.33     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 4512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.142: 526
       0.142 -    0.283: 93
       0.283 -    0.425: 5
       0.425 -    0.567: 25
       0.567 -    0.708: 13
  Chirality restraints: 662
  Sorted by residual:
  chirality pdb=" CG  LEU A 642 "
            pdb=" CB  LEU A 642 "
            pdb=" CD1 LEU A 642 "
            pdb=" CD2 LEU A 642 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.88   -0.71 2.00e-01 2.50e+01 1.25e+01
  chirality pdb=" CG  LEU B 418 "
            pdb=" CB  LEU B 418 "
            pdb=" CD1 LEU B 418 "
            pdb=" CD2 LEU B 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.88   -0.71 2.00e-01 2.50e+01 1.25e+01
  chirality pdb=" CG  LEU B 554 "
            pdb=" CB  LEU B 554 "
            pdb=" CD1 LEU B 554 "
            pdb=" CD2 LEU B 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.89   -0.70 2.00e-01 2.50e+01 1.21e+01
  ... (remaining 659 not shown)

  Planarity restraints: 1832
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 455 "   -0.289 2.00e-02 2.50e+03   1.03e-01 4.27e+02
        pdb=" CG  TRP A 455 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 455 "    0.062 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 455 "    0.052 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 455 "    0.109 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 455 "    0.027 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 455 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 455 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 455 "    0.028 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 455 "   -0.066 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 455 "   -0.010 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 455 "    0.109 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 455 "    0.113 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 455 "   -0.114 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 455 "    0.087 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 455 "   -0.102 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 583 "    0.218 2.00e-02 2.50e+03   7.18e-02 2.06e+02
        pdb=" CG  TRP A 583 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 583 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 583 "   -0.044 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 583 "   -0.072 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 583 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 583 "   -0.058 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 583 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 583 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 583 "    0.030 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 583 "   -0.038 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 583 "    0.030 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 583 "   -0.073 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 583 "    0.051 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 583 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 583 "    0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 500 "   -0.171 2.00e-02 2.50e+03   6.86e-02 1.88e+02
        pdb=" CG  TRP B 500 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 500 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 500 "    0.017 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 500 "    0.067 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 500 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 500 "    0.053 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 500 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 500 "    0.032 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 500 "   -0.037 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 500 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 500 "    0.111 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 500 "    0.086 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 500 "   -0.079 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 500 "    0.047 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 500 "   -0.065 2.00e-02 2.50e+03
  ... (remaining 1829 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.93: 171
        1.93 -     2.60: 9302
        2.60 -     3.26: 30667
        3.26 -     3.93: 38723
        3.93 -     4.60: 57554
  Nonbonded interactions: 136417
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 121 "
            pdb=" HD2 HIS A 354 "
     model   vdw
     1.261 2.450
  nonbonded pdb=" OE1 GLU B 600 "
            pdb=" H   GLU B 600 "
     model   vdw
     1.548 1.850
  nonbonded pdb=" OE1 GLU B 553 "
            pdb=" H   GLU B 553 "
     model   vdw
     1.563 1.850
  nonbonded pdb=" O   ILE A 192 "
            pdb=" H   ASP A 223 "
     model   vdw
     1.567 1.850
  nonbonded pdb=" H   ARG A 344 "
            pdb=" H   ARG A 345 "
     model   vdw
     1.583 2.100
  ... (remaining 136412 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=0.00 max=1.00 mean=0.99
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:             3.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.190
  Extract box with map and model:          13.130
  Check model and map are aligned:         0.150
  Set scattering table:                    0.100
  Process input model:                     37.910
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
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      :  0.016   0.123   5700  Z= 1.069
  Angle     :  1.941  15.617   7653  Z= 1.231
  Chirality :  0.169   0.708    662
  Planarity :  0.014   0.167   1074
  Dihedral  : 15.491 126.008   1961
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.74 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.46 %
    Favored  : 90.06 %
  Cbeta Deviations :  3.41 %
  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: -0.88 (0.29), residues: 802
  helix: -0.46 (0.28), residues: 324
  sheet:  0.24 (0.47), residues: 114
  loop : -0.86 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.191   0.027   TRP A 455 
   HIS   0.011   0.003   HIS A 539 
   PHE   0.115   0.016   PHE B 515 
   TYR   0.137   0.028   TYR A 512 
   ARG   0.012   0.002   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 148
  average time/residue: 0.5102
  time to fit residues: 91.8552
Evaluate side-chains
  115 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 1.126 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 4
  average time/residue: 0.4763
  time to fit residues: 3.9979
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6584
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5700  Z= 0.248
  Angle     :  0.657   5.950   7653  Z= 0.347
  Chirality :  0.044   0.151    662
  Planarity :  0.005   0.065   1074
  Dihedral  :  8.833 136.708    901
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.01 %
    Favored  : 83.09 %
  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: -0.38 (0.30), residues: 802
  helix:  0.26 (0.30), residues: 333
  sheet: -0.11 (0.44), residues: 133
  loop : -0.71 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP A 349 
   HIS   0.004   0.001   HIS A 613 
   PHE   0.016   0.002   PHE B 564 
   TYR   0.014   0.002   TYR A 512 
   ARG   0.003   0.001   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 128
  average time/residue: 0.4441
  time to fit residues: 70.3135
Evaluate side-chains
  121 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.824 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 5
  outliers final: 1
  residues processed: 5
  average time/residue: 0.1384
  time to fit residues: 2.1413
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:   30.0000
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:   30.0000
   chunk 73 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 25 optimal weight:   30.0000
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6632
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5700  Z= 0.233
  Angle     :  0.597   5.962   7653  Z= 0.313
  Chirality :  0.043   0.137    662
  Planarity :  0.004   0.038   1074
  Dihedral  :  8.116 137.941    901
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.60 %
    Favored  : 79.92 %
  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: -0.14 (0.31), residues: 802
  helix:  0.65 (0.31), residues: 331
  sheet:  0.01 (0.45), residues: 133
  loop : -0.80 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B 583 
   HIS   0.003   0.001   HIS A 613 
   PHE   0.014   0.002   PHE A 435 
   TYR   0.015   0.002   TYR A 512 
   ARG   0.005   0.001   ARG A 388 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 5
  residues processed: 122
  average time/residue: 0.4612
  time to fit residues: 69.4385
Evaluate side-chains
  113 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.887 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 5
  outliers final: 1
  residues processed: 5
  average time/residue: 0.1407
  time to fit residues: 2.3280
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 35 optimal weight:    0.2980
   chunk 49 optimal weight:    0.0670
   chunk 73 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 21 optimal weight:   50.0000
   chunk 65 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
A 571 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6624
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5700  Z= 0.205
  Angle     :  0.569   6.075   7653  Z= 0.295
  Chirality :  0.042   0.135    662
  Planarity :  0.004   0.038   1074
  Dihedral  :  7.744 141.228    901
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 19.03 %
    Favored  : 79.70 %
  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:  0.18 (0.32), residues: 802
  helix:  0.90 (0.31), residues: 330
  sheet:  0.02 (0.46), residues: 140
  loop : -0.53 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 561 
   HIS   0.002   0.001   HIS A 354 
   PHE   0.011   0.002   PHE A 406 
   TYR   0.012   0.002   TYR A 512 
   ARG   0.004   0.000   ARG A 445 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 117
  average time/residue: 0.4793
  time to fit residues: 68.7104
Evaluate side-chains
  113 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 4
  average time/residue: 0.1537
  time to fit residues: 2.0864
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 58 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 19 optimal weight:   30.0000
   chunk 26 optimal weight:   20.0000
   chunk 15 optimal weight:   50.0000
   overall best weight:    1.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5700  Z= 0.303
  Angle     :  0.612   6.139   7653  Z= 0.319
  Chirality :  0.043   0.147    662
  Planarity :  0.005   0.042   1074
  Dihedral  :  7.670 139.511    901
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.24 %
    Favored  : 79.28 %
  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:  0.09 (0.31), residues: 802
  helix:  0.94 (0.32), residues: 330
  sheet:  0.18 (0.46), residues: 132
  loop : -0.81 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP A 561 
   HIS   0.004   0.001   HIS A 613 
   PHE   0.015   0.003   PHE A 435 
   TYR   0.014   0.002   TYR A 538 
   ARG   0.004   0.001   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 112
  average time/residue: 0.5044
  time to fit residues: 68.9085
Evaluate side-chains
  109 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.751 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1545
  time to fit residues: 2.0298
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:   50.0000
   chunk 78 optimal weight:    0.9980
   chunk 65 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:   30.0000
   chunk 25 optimal weight:   30.0000
   chunk 41 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
B 537 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5700  Z= 0.200
  Angle     :  0.560   5.509   7653  Z= 0.289
  Chirality :  0.042   0.134    662
  Planarity :  0.004   0.035   1074
  Dihedral  :  7.504 139.591    901
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.76 %
    Favored  : 80.55 %
  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:  0.31 (0.32), residues: 802
  helix:  1.12 (0.32), residues: 330
  sheet:  0.14 (0.46), residues: 140
  loop : -0.63 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP A 349 
   HIS   0.003   0.001   HIS A 613 
   PHE   0.011   0.002   PHE B 515 
   TYR   0.023   0.002   TYR A 512 
   ARG   0.004   0.000   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 6
  residues processed: 113
  average time/residue: 0.4929
  time to fit residues: 67.8741
Evaluate side-chains
  106 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.840 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1316
  time to fit residues: 2.4989
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0050
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:   20.0000
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.4433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5700  Z= 0.196
  Angle     :  0.563   5.508   7653  Z= 0.291
  Chirality :  0.042   0.133    662
  Planarity :  0.004   0.036   1074
  Dihedral  :  7.408 138.565    901
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 18.82 %
    Favored  : 80.34 %
  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:  0.44 (0.32), residues: 802
  helix:  1.24 (0.32), residues: 331
  sheet:  0.17 (0.47), residues: 140
  loop : -0.55 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A 349 
   HIS   0.003   0.001   HIS B 613 
   PHE   0.010   0.002   PHE B 508 
   TYR   0.018   0.001   TYR A 512 
   ARG   0.005   0.000   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 105
  average time/residue: 0.4936
  time to fit residues: 63.1075
Evaluate side-chains
  102 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1108
  time to fit residues: 1.2567
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:   50.0000
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:   20.0000
   chunk 61 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 456 ASN
A 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5700  Z= 0.237
  Angle     :  0.579   6.273   7653  Z= 0.301
  Chirality :  0.043   0.138    662
  Planarity :  0.004   0.036   1074
  Dihedral  :  7.428 136.546    901
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 19.66 %
    Favored  : 79.07 %
  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:  0.38 (0.32), residues: 802
  helix:  1.26 (0.32), residues: 331
  sheet:  0.18 (0.47), residues: 137
  loop : -0.67 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP A 349 
   HIS   0.003   0.001   HIS A 613 
   PHE   0.013   0.002   PHE A 626 
   TYR   0.019   0.002   TYR A 512 
   ARG   0.005   0.001   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 103
  average time/residue: 0.4979
  time to fit residues: 63.0736
Evaluate side-chains
  101 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.845 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1420
  time to fit residues: 2.0689
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:   30.0000
   chunk 65 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5700  Z= 0.216
  Angle     :  0.566   5.351   7653  Z= 0.294
  Chirality :  0.042   0.136    662
  Planarity :  0.004   0.039   1074
  Dihedral  :  7.396 135.541    901
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 20.08 %
    Favored  : 79.70 %
  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:  0.46 (0.32), residues: 802
  helix:  1.31 (0.32), residues: 332
  sheet:  0.13 (0.47), residues: 139
  loop : -0.59 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP A 349 
   HIS   0.002   0.001   HIS A 613 
   PHE   0.010   0.002   PHE A 626 
   TYR   0.016   0.002   TYR A 512 
   ARG   0.005   0.000   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 98
  average time/residue: 0.5118
  time to fit residues: 61.3633
Evaluate side-chains
  98 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1220
  time to fit residues: 1.3795
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 80 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   chunk 64 optimal weight:    0.1980
   chunk 6 optimal weight:   20.0000
   chunk 49 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:   40.0000
   chunk 59 optimal weight:    0.6980
   chunk 9 optimal weight:   40.0000
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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: 0.6585
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5700  Z= 0.159
  Angle     :  0.532   5.378   7653  Z= 0.273
  Chirality :  0.041   0.134    662
  Planarity :  0.004   0.035   1074
  Dihedral  :  7.166 135.338    901
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 20.72 %
    Favored  : 79.07 %
  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:  0.76 (0.33), residues: 802
  helix:  1.50 (0.33), residues: 333
  sheet:  0.31 (0.48), residues: 141
  loop : -0.38 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A 561 
   HIS   0.002   0.001   HIS A 539 
   PHE   0.008   0.001   PHE B 508 
   TYR   0.012   0.001   TYR A 512 
   ARG   0.006   0.000   ARG B 606 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   45 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue MET   49 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue ILE   77 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue ALA   84 is missing expected H atoms. Skipping.
Residue ALA   85 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue TYR   90 is missing expected H atoms. Skipping.
Residue ILE   91 is missing expected H atoms. Skipping.
Residue VAL   93 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ALA   98 is missing expected H atoms. Skipping.
Residue SER  103 is missing expected H atoms. Skipping.
Residue LYS  105 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue MET  110 is missing expected H atoms. Skipping.
Residue MET  111 is missing expected H atoms. Skipping.
Residue ILE  112 is missing expected H atoms. Skipping.
Residue ALA  113 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  116 is missing expected H atoms. Skipping.
Residue VAL  117 is missing expected H atoms. Skipping.
Residue TYR  119 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  128 is missing expected H atoms. Skipping.
Residue THR  129 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue ILE  138 is missing expected H atoms. Skipping.
Residue THR  139 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue ALA  145 is missing expected H atoms. Skipping.
Residue LYS  146 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LYS  151 is missing expected H atoms. Skipping.
Residue ILE  153 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue ALA  155 is missing expected H atoms. Skipping.
Residue LEU  156 is missing expected H atoms. Skipping.
Residue TYR  174 is missing expected H atoms. Skipping.
Residue ALA  175 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LEU  178 is missing expected H atoms. Skipping.
Residue VAL  179 is missing expected H atoms. Skipping.
Residue LYS  180 is missing expected H atoms. Skipping.
Residue ILE  182 is missing expected H atoms. Skipping.
Residue SER  184 is missing expected H atoms. Skipping.
Residue TYR  189 is missing expected H atoms. Skipping.
Residue ILE  192 is missing expected H atoms. Skipping.
Residue VAL  194 is missing expected H atoms. Skipping.
Residue ALA  195 is missing expected H atoms. Skipping.
Residue TYR  197 is missing expected H atoms. Skipping.
Residue LYS  199 is missing expected H atoms. Skipping.
Residue ALA  204 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue ALA  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LYS  215 is missing expected H atoms. Skipping.
Residue LYS  217 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue SER  219 is missing expected H atoms. Skipping.
Residue ALA  220 is missing expected H atoms. Skipping.
Residue ALA  222 is missing expected H atoms. Skipping.
Residue ILE  225 is missing expected H atoms. Skipping.
Residue ILE  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue ALA  233 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  242 is missing expected H atoms. Skipping.
Residue THR  244 is missing expected H atoms. Skipping.
Residue MET  246 is missing expected H atoms. Skipping.
Residue ILE  248 is missing expected H atoms. Skipping.
Residue THR  249 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue VAL  253 is missing expected H atoms. Skipping.
Residue ILE  256 is missing expected H atoms. Skipping.
Residue ILE  259 is missing expected H atoms. Skipping.
Residue TYR  262 is missing expected H atoms. Skipping.
Residue SER  264 is missing expected H atoms. Skipping.
Residue LEU  265 is missing expected H atoms. Skipping.
Residue LEU  268 is missing expected H atoms. Skipping.
Residue VAL  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue SER  272 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  284 is missing expected H atoms. Skipping.
Residue ILE  287 is missing expected H atoms. Skipping.
Residue LYS  288 is missing expected H atoms. Skipping.
Residue ALA  292 is missing expected H atoms. Skipping.
Residue ALA  293 is missing expected H atoms. Skipping.
Residue ILE  294 is missing expected H atoms. Skipping.
Residue TYR  297 is missing expected H atoms. Skipping.
Residue ILE  299 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  302 is missing expected H atoms. Skipping.
Residue VAL  303 is missing expected H atoms. Skipping.
Residue SER  304 is missing expected H atoms. Skipping.
Residue LEU  305 is missing expected H atoms. Skipping.
Residue LEU  309 is missing expected H atoms. Skipping.
Residue LEU  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue SER  312 is missing expected H atoms. Skipping.
Residue LEU  314 is missing expected H atoms. Skipping.
Residue VAL  315 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue TYR  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  323 is missing expected H atoms. Skipping.
Residue MET  327 is missing expected H atoms. Skipping.
Residue ALA  328 is missing expected H atoms. Skipping.
Residue THR  329 is missing expected H atoms. Skipping.
Residue THR  330 is missing expected H atoms. Skipping.
Residue VAL  332 is missing expected H atoms. Skipping.
Residue LEU  333 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue LEU  336 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.4974
  time to fit residues: 61.0745
Evaluate side-chains
  100 residues out of total 716 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1187
  time to fit residues: 1.2469
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:   50.0000
   chunk 64 optimal weight:    0.9990
   chunk 26 optimal weight:   30.0000
   chunk 66 optimal weight:    0.6980
   chunk 8 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 56 optimal weight:    0.7980
   chunk 3 optimal weight:   30.0000
   chunk 46 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.229223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.187842 restraints weight = 16761.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 2.30
r_work: 0.4178 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.4017 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5700  Z= 0.215
  Angle     :  0.550   5.378   7653  Z= 0.286
  Chirality :  0.042   0.136    662
  Planarity :  0.004   0.035   1074
  Dihedral  :  7.213 133.940    901
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 20.93 %
    Favored  : 78.86 %
  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:  0.67 (0.32), residues: 802
  helix:  1.43 (0.32), residues: 335
  sheet:  0.58 (0.48), residues: 131
  loop : -0.57 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP A 349 
   HIS   0.003   0.001   HIS A 613 
   PHE   0.013   0.002   PHE A 626 
   TYR   0.017   0.002   TYR A 512 
   ARG   0.005   0.000   ARG B 606 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3651.80 seconds
wall clock time: 65 minutes 1.01 seconds (3901.01 seconds total)