Starting phenix.real_space_refine
on Mon Mar 11 09:18:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7u_32348/03_2024/7w7u_32348_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7u_32348/03_2024/7w7u_32348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7u_32348/03_2024/7w7u_32348.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7u_32348/03_2024/7w7u_32348.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7u_32348/03_2024/7w7u_32348_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7u_32348/03_2024/7w7u_32348_updated.pdb"
  }
  resolution = 3.0
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      58      5.16       5
     Be      1      3.05       5
     C    4996      2.51       5
     N    1306      2.21       5
     O    1468      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   16": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  152": "OE1" <-> "OE2"
    Residue "A ASP  157": "OD1" <-> "OD2"
    Residue "A TYR  295": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  367": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  394": "OE1" <-> "OE2"
    Residue "A GLU  412": "OE1" <-> "OE2"
    Residue "A ASP  426": "OD1" <-> "OD2"
    Residue "A PHE  483": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  737": "OD1" <-> "OD2"
    Residue "A TYR  836": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  891": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7833
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1017, 7833
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'peptide': 1015, 'undetermined': 2}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 46, 'TRANS': 968, None: 2}
            Not linked:
              pdbres="SER A1042 "
              pdbres="BEF A2001 "
            Not linked:
              pdbres="BEF A2001 "
              pdbres=" MG A2002 "
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 4.53, per 1000 atoms: 0.58
  Number of scatterers: 7833
  At special positions: 0
  Unit cell: (105.825, 85.905, 136.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      58     16.00
     Mg      1     11.99
     F       3      9.00
     O    1468      8.00
     N    1306      7.00
     C    4996      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.86
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      41 helices and 8 sheets defined
      48.2% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 6
      No H-bonds generated for 'chain 'A' and resid 4 through 6'
    Processing helix  chain 'A' and resid 9 through 16
    Processing helix  chain 'A' and resid 26 through 36
      removed outlier: 3.552A  pdb=" N   ARG A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 3.707A  pdb=" N   GLU A  58 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 78
      removed outlier: 3.614A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
      No H-bonds generated for 'chain 'A' and resid 84 through 87'
    Processing helix  chain 'A' and resid 89 through 116
      removed outlier: 3.594A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 231 through 241
    Processing helix  chain 'A' and resid 248 through 275
      removed outlier: 3.851A  pdb=" N   ASN A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 306
      removed outlier: 3.758A  pdb=" N   ALA A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 329
      removed outlier: 3.640A  pdb=" N   LYS A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
      removed outlier: 4.686A  pdb=" N   LEU A 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 419
    Processing helix  chain 'A' and resid 440 through 451
    Processing helix  chain 'A' and resid 464 through 467
      No H-bonds generated for 'chain 'A' and resid 464 through 467'
    Processing helix  chain 'A' and resid 471 through 478
    Processing helix  chain 'A' and resid 517 through 522
    Processing helix  chain 'A' and resid 538 through 553
    Processing helix  chain 'A' and resid 580 through 586
    Processing helix  chain 'A' and resid 607 through 615
    Processing helix  chain 'A' and resid 628 through 638
    Processing helix  chain 'A' and resid 654 through 658
    Processing helix  chain 'A' and resid 662 through 671
    Processing helix  chain 'A' and resid 680 through 693
      removed outlier: 3.688A  pdb=" N   PHE A 693 " --> pdb=" O   PHE A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 712
      Proline residue:  A 708  - end of helix
    Processing helix  chain 'A' and resid 724 through 728
    Processing helix  chain 'A' and resid 739 through 780
      removed outlier: 3.830A  pdb=" N   LEU A 780 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 796
    Processing helix  chain 'A' and resid 800 through 808
      removed outlier: 3.849A  pdb=" N   PHE A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 817
      No H-bonds generated for 'chain 'A' and resid 815 through 817'
    Processing helix  chain 'A' and resid 830 through 854
      removed outlier: 3.709A  pdb=" N   LEU A 837 " --> pdb=" O   PHE A 833 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 870
    Processing helix  chain 'A' and resid 883 through 889
      removed outlier: 3.616A  pdb=" N   ALA A 888 " --> pdb=" O   GLY A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 914
    Processing helix  chain 'A' and resid 930 through 948
    Processing helix  chain 'A' and resid 952 through 955
      No H-bonds generated for 'chain 'A' and resid 952 through 955'
    Processing helix  chain 'A' and resid 963 through 989
      Proline residue:  A 975  - end of helix
      removed outlier: 3.801A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1029
      Proline residue:  A1024  - end of helix
    Processing sheet with id=  A, first strand: chain 'A' and resid 126 through 129
    Processing sheet with id=  B, first strand: chain 'A' and resid 150 through 153
      removed outlier: 7.148A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 331 through 333
      removed outlier: 3.724A  pdb=" N   ILE A 715 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ARG A 619 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   SER A 350 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ILE A 621 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 425 through 427
    Processing sheet with id=  E, first strand: chain 'A' and resid 377 through 383
      removed outlier: 3.784A  pdb=" N   ARG A 371 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ASN A 380 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   PHE A 382 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   PHE A 367 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLY A 597 " --> pdb=" O   CYS A 364 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   MET A 366 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS A 595 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   ILE A 368 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   VAL A 593 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 13.114A  pdb=" N   ASP A 370 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.300A  pdb=" N   THR A 591 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 532 through 535
      removed outlier: 6.763A  pdb=" N   LEU A 590 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   ILE A 527 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   PHE A 592 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   VAL A 529 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 651 through 653
      removed outlier: 6.382A  pdb=" N   CYS A 674 " --> pdb=" O   PHE A 652 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  G
    Processing sheet with id=  H, first strand: chain 'A' and resid 173 through 176
      removed outlier: 6.032A  pdb=" N   ASP A 176 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ILE A 214 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)

    357 hydrogen bonds defined for protein.
    915 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: 2.78

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2555
        1.34 -     1.46: 1611
        1.46 -     1.58: 3724
        1.58 -     1.70: 0
        1.70 -     1.81: 90
  Bond restraints: 7980
  Sorted by residual:
  bond pdb=" BE  BEF A2001 "
       pdb=" F2  BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.560 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" BE  BEF A2001 "
       pdb=" F3  BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.548 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" BE  BEF A2001 "
       pdb=" F1  BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.532 -0.056 2.00e-02 2.50e+03 7.75e+00
  bond pdb=" CB  PRO A 960 "
       pdb=" CG  PRO A 960 "
    ideal  model  delta    sigma   weight residual
    1.492  1.549 -0.057 5.00e-02 4.00e+02 1.30e+00
  bond pdb=" CA  ASP A 490 "
       pdb=" C   ASP A 490 "
    ideal  model  delta    sigma   weight residual
    1.523  1.510  0.012 1.41e-02 5.03e+03 7.39e-01
  ... (remaining 7975 not shown)

  Histogram of bond angle deviations from ideal:
       99.21 -   106.17: 219
      106.17 -   113.14: 4445
      113.14 -   120.11: 2704
      120.11 -   127.07: 3376
      127.07 -   134.04: 87
  Bond angle restraints: 10831
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb=" BE  BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.98   12.98 3.00e+00 1.11e-01 1.87e+01
  angle pdb=" F1  BEF A2001 "
        pdb=" BE  BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.70   10.42 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" F1  BEF A2001 "
        pdb=" BE  BEF A2001 "
        pdb=" F2  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.91  111.64    8.27 3.00e+00 1.11e-01 7.61e+00
  angle pdb=" C   ARG A 835 "
        pdb=" N   TYR A 836 "
        pdb=" CA  TYR A 836 "
      ideal   model   delta    sigma   weight residual
     120.72  116.41    4.31 1.67e+00 3.59e-01 6.65e+00
  angle pdb=" C   GLN A 758 "
        pdb=" N   PHE A 759 "
        pdb=" CA  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     121.14  117.16    3.98 1.75e+00 3.27e-01 5.17e+00
  ... (remaining 10826 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 4423
       17.06 -    34.12: 333
       34.12 -    51.18: 60
       51.18 -    68.23: 12
       68.23 -    85.29: 5
  Dihedral angle restraints: 4833
    sinusoidal: 1900
      harmonic: 2933
  Sorted by residual:
  dihedral pdb=" CB  CYS A 875 "
           pdb=" SG  CYS A 875 "
           pdb=" SG  CYS A 887 "
           pdb=" CB  CYS A 887 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.87   44.87     1      1.00e+01 1.00e-02 2.80e+01
  dihedral pdb=" CA  ARG A 571 "
           pdb=" C   ARG A 571 "
           pdb=" N   ARG A 572 "
           pdb=" CA  ARG A 572 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.68  -20.32     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" SG  CYS A 875 "
           pdb=" CB  CYS A 887 "
           pdb=" SG  CYS A 887 "
           pdb=" CA  CYS A 887 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    8.78   70.22     1      2.00e+01 2.50e-03 1.59e+01
  ... (remaining 4830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 821
       0.032 -    0.063: 293
       0.063 -    0.095: 100
       0.095 -    0.127: 54
       0.127 -    0.158: 4
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  PHE A 759 "
            pdb=" N   PHE A 759 "
            pdb=" C   PHE A 759 "
            pdb=" CB  PHE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 623 "
            pdb=" N   ILE A 623 "
            pdb=" C   ILE A 623 "
            pdb=" CB  ILE A 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 1269 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 959 "    0.065 5.00e-02 4.00e+02   9.82e-02 1.54e+01
        pdb=" N   PRO A 960 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 960 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 960 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 759 "   -0.012 2.00e-02 2.50e+03   1.24e-02 2.71e+00
        pdb=" CG  PHE A 759 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 759 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 759 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 759 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 534 "   -0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO A 535 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 43
        2.55 -     3.14: 6349
        3.14 -     3.73: 12601
        3.73 -     4.31: 17053
        4.31 -     4.90: 28492
  Nonbonded interactions: 64538
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     1.966 2.170
  nonbonded pdb=" F3  BEF A2001 "
            pdb="MG    MG A2002 "
     model   vdw
     2.078 2.120
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.086 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.129 2.170
  nonbonded pdb=" OG  SER A 555 "
            pdb=" OE1 GLN A 643 "
     model   vdw
     2.281 2.440
  ... (remaining 64533 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.590
  Check model and map are aligned:         0.120
  Set scattering table:                    0.090
  Process input model:                     24.570
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
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      :  0.003   0.084   7980  Z= 0.193
  Angle     :  0.559  12.976  10831  Z= 0.295
  Chirality :  0.041   0.158   1272
  Planarity :  0.005   0.098   1379
  Dihedral  : 12.540  85.292   2928
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  0.77 (0.27), residues: 1009
  helix:  1.37 (0.23), residues: 505
  sheet: -0.49 (0.52), residues: 100
  loop : -0.21 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 966 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 294 
 ARG   0.005   0.000   ARG A 198 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6800 (ptp-170) cc_final: 0.6591 (ptp-170)
REVERT: A  467 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.6975 (tpt-90)
REVERT: A  477 GLN cc_start: 0.5667 (tp40) cc_final: 0.5370 (mm110)
REVERT: A  650 LYS cc_start: 0.8185 (mttp) cc_final: 0.7981 (mtmt)
REVERT: A  756 MET cc_start: 0.7879 (ttm) cc_final: 0.7495 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 1.2819
  time to fit residues: 202.9537
Evaluate side-chains
  107 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0060
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 58 optimal weight:    0.1980
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 615 GLN
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7980  Z= 0.141
  Angle     :  0.479   5.770  10831  Z= 0.260
  Chirality :  0.040   0.153   1272
  Planarity :  0.005   0.070   1379
  Dihedral  :  3.756  16.999   1072
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.47 %
    Favored  : 85.52 %
  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:  0.81 (0.27), residues: 1009
  helix:  1.38 (0.24), residues: 511
  sheet: -0.42 (0.51), residues: 95
  loop : -0.22 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.023   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 571 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A   90 GLU cc_start: 0.7051 (tp30) cc_final: 0.6841 (tp30)
REVERT: A  467 ARG cc_start: 0.7384 (tpt-90) cc_final: 0.7102 (tpt-90)
REVERT: A  477 GLN cc_start: 0.5635 (tp40) cc_final: 0.5338 (mm110)
REVERT: A  480 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7135 (ptmt)
REVERT: A  536 MET cc_start: 0.6456 (tpt) cc_final: 0.6161 (tpt)
REVERT: A  650 LYS cc_start: 0.8241 (mttp) cc_final: 0.8008 (mtmt)
  outliers start: 26
  outliers final: 9
  residues processed: 130
  average time/residue: 1.2745
  time to fit residues: 175.1165
Evaluate side-chains
  114 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0570
   chunk 76 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0060
   chunk 25 optimal weight:    4.9990
   chunk 91 optimal weight:    9.9990
   chunk 99 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.7916

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

Flipped N/Q/H residues before XYZ refinement:
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7980  Z= 0.147
  Angle     :  0.462   5.326  10831  Z= 0.249
  Chirality :  0.040   0.164   1272
  Planarity :  0.005   0.062   1379
  Dihedral  :  3.704  16.363   1072
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.21 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.27), residues: 1009
  helix:  1.24 (0.24), residues: 518
  sheet: -0.37 (0.50), residues: 94
  loop : -0.22 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.024   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.007   0.000   ARG A 571 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   90 GLU cc_start: 0.7073 (tp30) cc_final: 0.6746 (tp30)
REVERT: A  467 ARG cc_start: 0.7437 (tpt-90) cc_final: 0.7123 (tpt-90)
REVERT: A  480 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7185 (ptmt)
REVERT: A  536 MET cc_start: 0.6405 (tpt) cc_final: 0.6049 (tpt)
REVERT: A  650 LYS cc_start: 0.8200 (mttp) cc_final: 0.7965 (mtmt)
REVERT: A  917 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6704 (tp30)
  outliers start: 29
  outliers final: 9
  residues processed: 128
  average time/residue: 1.1375
  time to fit residues: 154.8564
Evaluate side-chains
  111 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0170
   chunk 26 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7980  Z= 0.164
  Angle     :  0.481   6.483  10831  Z= 0.256
  Chirality :  0.041   0.172   1272
  Planarity :  0.005   0.058   1379
  Dihedral  :  3.744  15.566   1072
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 14.72 %
    Favored  : 81.69 %
  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:  0.65 (0.27), residues: 1009
  helix:  1.17 (0.24), residues: 521
  sheet: -0.34 (0.49), residues: 94
  loop : -0.24 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 943 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 139 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A   90 GLU cc_start: 0.7020 (tp30) cc_final: 0.6619 (tp30)
REVERT: A  120 LYS cc_start: 0.6401 (mmtt) cc_final: 0.6197 (mmtp)
REVERT: A  400 LYS cc_start: 0.7821 (pptt) cc_final: 0.7581 (pptt)
REVERT: A  467 ARG cc_start: 0.7454 (tpt-90) cc_final: 0.7119 (tpt-90)
REVERT: A  480 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7132 (ptmt)
REVERT: A  536 MET cc_start: 0.6063 (tpt) cc_final: 0.5612 (tpt)
REVERT: A  732 MET cc_start: 0.8286 (ttm) cc_final: 0.8079 (ttm)
REVERT: A  839 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7321 (mt)
REVERT: A  917 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6718 (tp30)
  outliers start: 31
  outliers final: 15
  residues processed: 122
  average time/residue: 1.2419
  time to fit residues: 160.8081
Evaluate side-chains
  120 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  665 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  924 MET
Chi-restraints excluded: chain A residue  963 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0670
   chunk 40 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7524

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7980  Z= 0.142
  Angle     :  0.457   6.491  10831  Z= 0.244
  Chirality :  0.040   0.180   1272
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.673  14.995   1072
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.57 %
    Favored  : 80.88 %
  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:  0.69 (0.27), residues: 1009
  helix:  1.23 (0.24), residues: 521
  sheet: -0.30 (0.49), residues: 94
  loop : -0.28 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.024   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 571 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A   90 GLU cc_start: 0.6898 (tp30) cc_final: 0.6532 (tm-30)
REVERT: A  467 ARG cc_start: 0.7411 (tpt-90) cc_final: 0.7088 (tpt-90)
REVERT: A  480 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7113 (ptmt)
REVERT: A  536 MET cc_start: 0.6073 (tpt) cc_final: 0.5598 (tpt)
REVERT: A  732 MET cc_start: 0.8268 (ttm) cc_final: 0.8036 (ttm)
REVERT: A  917 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6808 (tp30)
  outliers start: 22
  outliers final: 13
  residues processed: 119
  average time/residue: 1.1680
  time to fit residues: 147.6168
Evaluate side-chains
  117 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  665 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  963 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0980
   chunk 24 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 576 HIS
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7980  Z= 0.152
  Angle     :  0.457   5.170  10831  Z= 0.246
  Chirality :  0.040   0.182   1272
  Planarity :  0.005   0.055   1379
  Dihedral  :  3.676  14.179   1072
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.03 %
    Favored  : 80.19 %
  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:  0.69 (0.26), residues: 1009
  helix:  1.23 (0.24), residues: 521
  sheet: -0.31 (0.49), residues: 94
  loop : -0.27 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 943 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 571 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  467 ARG cc_start: 0.7291 (tpt-90) cc_final: 0.7073 (tpt-90)
REVERT: A  480 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7005 (ptmt)
REVERT: A  536 MET cc_start: 0.6111 (tpt) cc_final: 0.5645 (tpt)
REVERT: A  732 MET cc_start: 0.8295 (ttm) cc_final: 0.8040 (ttm)
REVERT: A  816 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7499 (mmp)
REVERT: A  839 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7303 (mt)
REVERT: A  917 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6855 (tp30)
  outliers start: 24
  outliers final: 15
  residues processed: 117
  average time/residue: 1.2518
  time to fit residues: 155.1132
Evaluate side-chains
  116 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  665 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  816 MET
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  963 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7980  Z= 0.227
  Angle     :  0.513   5.287  10831  Z= 0.274
  Chirality :  0.043   0.185   1272
  Planarity :  0.005   0.054   1379
  Dihedral  :  3.967  15.405   1072
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.50 %
    Favored  : 79.61 %
  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:  0.43 (0.26), residues: 1009
  helix:  0.95 (0.23), residues: 527
  sheet: -0.02 (0.52), residues: 82
  loop : -0.43 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 288 
 HIS   0.002   0.001   HIS A  15 
 PHE   0.027   0.002   PHE A 759 
 TYR   0.010   0.002   TYR A 842 
 ARG   0.002   0.000   ARG A 571 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   90 GLU cc_start: 0.7014 (tp30) cc_final: 0.6672 (tm-30)
REVERT: A  480 LYS cc_start: 0.7448 (mtmt) cc_final: 0.6919 (ptmt)
REVERT: A  536 MET cc_start: 0.6230 (tpt) cc_final: 0.5772 (tpt)
REVERT: A  732 MET cc_start: 0.8356 (ttm) cc_final: 0.7975 (ttm)
REVERT: A  816 MET cc_start: 0.8068 (mmm) cc_final: 0.7749 (mmp)
REVERT: A  917 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6742 (tp30)
  outliers start: 25
  outliers final: 14
  residues processed: 124
  average time/residue: 1.1716
  time to fit residues: 154.5708
Evaluate side-chains
  117 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue  969 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    0.4980
   chunk 66 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 93 optimal weight:    0.7980
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7980  Z= 0.147
  Angle     :  0.466   5.514  10831  Z= 0.252
  Chirality :  0.041   0.198   1272
  Planarity :  0.005   0.055   1379
  Dihedral  :  3.775  14.523   1072
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.00 %
    Favored  : 78.68 %
  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:  0.56 (0.26), residues: 1009
  helix:  1.11 (0.23), residues: 526
  sheet: -0.16 (0.52), residues: 84
  loop : -0.40 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 943 
 PHE   0.024   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 836 
 ARG   0.005   0.000   ARG A 467 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  480 LYS cc_start: 0.7202 (mtmt) cc_final: 0.6781 (ptmt)
REVERT: A  536 MET cc_start: 0.6201 (tpt) cc_final: 0.5721 (tpt)
REVERT: A  732 MET cc_start: 0.8325 (ttm) cc_final: 0.8044 (ttm)
REVERT: A  816 MET cc_start: 0.7982 (mmm) cc_final: 0.7671 (mmp)
REVERT: A  839 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7391 (mt)
REVERT: A  917 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6934 (tp30)
  outliers start: 20
  outliers final: 10
  residues processed: 116
  average time/residue: 1.1031
  time to fit residues: 136.5332
Evaluate side-chains
  114 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  917 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0020
   chunk 85 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0970
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7980  Z= 0.135
  Angle     :  0.466   8.717  10831  Z= 0.247
  Chirality :  0.040   0.197   1272
  Planarity :  0.005   0.055   1379
  Dihedral  :  3.674  13.323   1072
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.47 %
    Favored  : 78.33 %
  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:  0.63 (0.27), residues: 1009
  helix:  1.22 (0.23), residues: 526
  sheet: -0.50 (0.49), residues: 94
  loop : -0.33 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.023   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 836 
 ARG   0.005   0.000   ARG A 467 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  442 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6821 (mt-10)
REVERT: A  480 LYS cc_start: 0.6946 (mtmt) cc_final: 0.6604 (ptmt)
REVERT: A  536 MET cc_start: 0.6164 (tpt) cc_final: 0.5746 (tpt)
REVERT: A  732 MET cc_start: 0.8312 (ttm) cc_final: 0.8055 (ttm)
REVERT: A  816 MET cc_start: 0.8019 (mmm) cc_final: 0.7714 (mmp)
REVERT: A  839 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7348 (mt)
REVERT: A  917 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6972 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 113
  average time/residue: 1.2181
  time to fit residues: 146.3874
Evaluate side-chains
  113 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  665 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  917 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7980  Z= 0.220
  Angle     :  0.518   9.557  10831  Z= 0.274
  Chirality :  0.043   0.208   1272
  Planarity :  0.005   0.053   1379
  Dihedral  :  3.901  15.131   1072
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.58 %
    Favored  : 78.56 %
  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:  0.40 (0.26), residues: 1009
  helix:  0.95 (0.23), residues: 535
  sheet: -0.19 (0.52), residues: 82
  loop : -0.48 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 551 
 HIS   0.003   0.001   HIS A 943 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.011   0.002   TYR A 842 
 ARG   0.005   0.000   ARG A 467 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  442 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6881 (mt-10)
REVERT: A  480 LYS cc_start: 0.6884 (mtmt) cc_final: 0.6511 (ptmt)
REVERT: A  536 MET cc_start: 0.6233 (tpt) cc_final: 0.5812 (tpt)
REVERT: A  732 MET cc_start: 0.8363 (ttm) cc_final: 0.8072 (ttm)
REVERT: A  816 MET cc_start: 0.8019 (mmm) cc_final: 0.7737 (mmp)
REVERT: A  839 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7526 (mt)
REVERT: A  917 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6902 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 112
  average time/residue: 1.1992
  time to fit residues: 142.8413
Evaluate side-chains
  110 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  839 ILE
Chi-restraints excluded: chain A residue  917 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0670
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 919 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.179278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.140584 restraints weight = 8222.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.63
r_work: 0.3249 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7980  Z= 0.138
  Angle     :  0.470   8.969  10831  Z= 0.250
  Chirality :  0.041   0.201   1272
  Planarity :  0.005   0.055   1379
  Dihedral  :  3.701  12.972   1072
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.16 %
    Favored  : 78.22 %
  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:  0.60 (0.26), residues: 1009
  helix:  1.20 (0.23), residues: 526
  sheet: -0.30 (0.52), residues: 84
  loop : -0.43 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 107 
 HIS   0.002   0.000   HIS A 943 
 PHE   0.023   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 836 
 ARG   0.005   0.000   ARG A 467 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3171.10 seconds
wall clock time: 57 minutes 9.73 seconds (3429.73 seconds total)