Starting phenix.real_space_refine
on Tue Sep 24 03:05:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/09_2024/7mfe_23814.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/09_2024/7mfe_23814.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/09_2024/7mfe_23814.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/09_2024/7mfe_23814.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/09_2024/7mfe_23814.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/09_2024/7mfe_23814.cif"
  }
  resolution = 4.07
  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=   0.001 sd=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      41      5.16       5
     C    4333      2.51       5
     N    1184      2.21       5
     O    1282      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6844
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3291
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 390}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1785
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 1766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1766
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    673  SG  CYS A 248      50.552  27.800  52.225  1.00 14.22           S
  ATOM    808  SG  CYS A 264      42.464  38.382  45.422  1.00 19.76           S

  Time building chain proxies: 4.46, per 1000 atoms: 0.65
  Number of scatterers: 6844
  At special positions: 0
  Unit cell: (99.752, 74.14, 111.884, 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)
     Zn      2     29.99
     S      41     16.00
     P       2     15.00
     O    1282      8.00
     N    1184      7.00
     C    4333      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 949.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" ND1 HIS A 269 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 248 "
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" ND1 HIS A 235 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 264 "


  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      60.4% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 178 through 188
      removed outlier: 4.045A  pdb=" N   ALA A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   MET A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   ARG A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 217
      removed outlier: 4.407A  pdb=" N   TRP A 216 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 506
      removed outlier: 3.918A  pdb=" N   GLN A 496 " --> pdb=" O   PRO A 492 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL A 504 " --> pdb=" O   ASN A 500 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A 505 " --> pdb=" O   GLU A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 543
      removed outlier: 3.807A  pdb=" N   ILE A 543 " --> pdb=" O   HIS A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 570
      removed outlier: 3.916A  pdb=" N   LEU A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A 554 " --> pdb=" O   MET A 550 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ALA A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 627
      removed outlier: 5.491A  pdb=" N   MET A 627 " --> pdb=" O   GLU A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 3.609A  pdb=" N   GLU A 648 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLY A 652 " --> pdb=" O   GLU A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 672
      removed outlier: 3.606A  pdb=" N   ILE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE A 667 " --> pdb=" O   ASP A 663 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG A 671 " --> pdb=" O   PHE A 667 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   GLY A 672 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 681
      removed outlier: 3.692A  pdb=" N   LYS A 680 " --> pdb=" O   ASP A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 697
      removed outlier: 3.576A  pdb=" N   ALA A 694 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 720
      removed outlier: 3.610A  pdb=" N   ILE A 714 " --> pdb=" O   ILE A 710 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU A 715 " --> pdb=" O   LEU A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 725
      removed outlier: 3.799A  pdb=" N   ILE A 724 " --> pdb=" O   LEU A 721 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   HIS A 725 " --> pdb=" O   PRO A 722 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 721 through 725'
    Processing helix  chain 'C' and resid 3 through 16
      removed outlier: 3.909A  pdb=" N   ALA C  16 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 31
      removed outlier: 3.543A  pdb=" N   SER C  28 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 68
      removed outlier: 3.995A  pdb=" N   LEU C  43 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR C  48 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER C  64 " --> pdb=" O   ARG C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 104
    Processing helix  chain 'C' and resid 111 through 131
      removed outlier: 3.600A  pdb=" N   TYR C 118 " --> pdb=" O   SER C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 137
    Processing helix  chain 'C' and resid 138 through 160
      removed outlier: 3.640A  pdb=" N   GLN C 144 " --> pdb=" O   GLY C 140 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE C 155 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   MET C 160 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 180
      removed outlier: 3.633A  pdb=" N   LEU C 168 " --> pdb=" O   HIS C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 198
    Processing helix  chain 'C' and resid 210 through 230
      removed outlier: 4.233A  pdb=" N   SER C 214 " --> pdb=" O   SER C 210 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG C 222 " --> pdb=" O   MET C 218 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN C 224 " --> pdb=" O   LEU C 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 15
      removed outlier: 3.573A  pdb=" N   ALA B  10 " --> pdb=" O   LEU B   6 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA B  13 " --> pdb=" O   LYS B   9 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLN B  15 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 31
      removed outlier: 3.535A  pdb=" N   GLU B  31 " --> pdb=" O   LYS B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 67
      removed outlier: 3.535A  pdb=" N   SER B  45 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG B  55 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 104
      removed outlier: 4.305A  pdb=" N   VAL B  97 " --> pdb=" O   ILE B  93 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 133
      removed outlier: 3.573A  pdb=" N   GLY B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 160
      removed outlier: 3.881A  pdb=" N   LYS B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 181
    Processing helix  chain 'B' and resid 184 through 203
    Processing helix  chain 'B' and resid 207 through 230
      removed outlier: 4.006A  pdb=" N   LYS B 212 " --> pdb=" O   GLU B 208 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   ASP B 213 " --> pdb=" O   GLU B 209 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU B 216 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   SER B 230 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 160
      removed outlier: 3.520A  pdb=" N   VAL A 169 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   VAL A 159 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 167 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208
      removed outlier: 4.204A  pdb=" N   VAL A 197 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   TYR A 198 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   HIS A 223 " --> pdb=" O   TYR A 198 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 241
      removed outlier: 3.782A  pdb=" N   GLY A 258 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462
      removed outlier: 5.120A  pdb=" N   LYS A 473 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 479 through 483
      removed outlier: 6.214A  pdb=" N   GLN A 530 " --> pdb=" O   PHE A 516 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   PHE A 516 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 585
      removed outlier: 4.155A  pdb=" N   THR A 589 " --> pdb=" O   HIS A 585 " (cutoff:3.500A)

    364 hydrogen bonds defined for protein.
    1071 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: 1.96

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2248
        1.34 -     1.46: 1537
        1.46 -     1.58: 3103
        1.58 -     1.70: 8
        1.70 -     1.82: 65
  Bond restraints: 6961
  Sorted by residual:
  bond pdb=" N   VAL B  97 "
       pdb=" CA  VAL B  97 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 1.21e-02 6.83e+03 7.76e+00
  bond pdb=" N   LEU B  98 "
       pdb=" CA  LEU B  98 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.21e-02 6.83e+03 7.39e+00
  bond pdb=" N   CYS B  94 "
       pdb=" CA  CYS B  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.30e-02 5.92e+03 7.18e+00
  bond pdb=" N   SER B  99 "
       pdb=" CA  SER B  99 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.45e+00
  bond pdb=" N   ASN B  95 "
       pdb=" CA  ASN B  95 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.33e-02 5.65e+03 5.17e+00
  ... (remaining 6956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 9037
        1.37 -     2.74: 285
        2.74 -     4.11: 45
        4.11 -     5.47: 15
        5.47 -     6.84: 3
  Bond angle restraints: 9385
  Sorted by residual:
  angle pdb=" N   ASP B  96 "
        pdb=" CA  ASP B  96 "
        pdb=" C   ASP B  96 "
      ideal   model   delta    sigma   weight residual
     111.07  105.23    5.84 1.07e+00 8.73e-01 2.98e+01
  angle pdb=" N   CYS B  94 "
        pdb=" CA  CYS B  94 "
        pdb=" C   CYS B  94 "
      ideal   model   delta    sigma   weight residual
     113.55  108.64    4.91 1.26e+00 6.30e-01 1.52e+01
  angle pdb=" N   ASN B  95 "
        pdb=" CA  ASN B  95 "
        pdb=" C   ASN B  95 "
      ideal   model   delta    sigma   weight residual
     112.54  107.85    4.69 1.22e+00 6.72e-01 1.48e+01
  angle pdb=" CA  VAL B  97 "
        pdb=" C   VAL B  97 "
        pdb=" O   VAL B  97 "
      ideal   model   delta    sigma   weight residual
     120.85  117.20    3.65 1.06e+00 8.90e-01 1.19e+01
  angle pdb=" N   LEU B 100 "
        pdb=" CA  LEU B 100 "
        pdb=" C   LEU B 100 "
      ideal   model   delta    sigma   weight residual
     111.28  107.75    3.53 1.09e+00 8.42e-01 1.05e+01
  ... (remaining 9380 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3782
       17.94 -    35.88: 384
       35.88 -    53.82: 63
       53.82 -    71.76: 19
       71.76 -    89.69: 8
  Dihedral angle restraints: 4256
    sinusoidal: 1730
      harmonic: 2526
  Sorted by residual:
  dihedral pdb=" CA  GLU C 209 "
           pdb=" C   GLU C 209 "
           pdb=" N   SER C 210 "
           pdb=" CA  SER C 210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.10  -25.90     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  MET A 620 "
           pdb=" C   MET A 620 "
           pdb=" N   ALA A 621 "
           pdb=" CA  ALA A 621 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.09  -21.91     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  GLN C  15 "
           pdb=" C   GLN C  15 "
           pdb=" N   ALA C  16 "
           pdb=" CA  ALA C  16 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4253 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 832
       0.045 -    0.090: 173
       0.090 -    0.134: 36
       0.134 -    0.179: 2
       0.179 -    0.224: 2
  Chirality restraints: 1045
  Sorted by residual:
  chirality pdb=" CA  LEU B 100 "
            pdb=" N   LEU B 100 "
            pdb=" C   LEU B 100 "
            pdb=" CB  LEU B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ASP B  96 "
            pdb=" N   ASP B  96 "
            pdb=" C   ASP B  96 "
            pdb=" CB  ASP B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  CYS B  94 "
            pdb=" N   CYS B  94 "
            pdb=" C   CYS B  94 "
            pdb=" CB  CYS B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.96e-01
  ... (remaining 1042 not shown)

  Planarity restraints: 1198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 191 "   -0.036 5.00e-02 4.00e+02   5.46e-02 4.78e+00
        pdb=" N   PRO A 192 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 192 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 192 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 621 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.52e+00
        pdb=" N   PRO A 622 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 622 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 622 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 707 "    0.033 5.00e-02 4.00e+02   5.02e-02 4.04e+00
        pdb=" N   PRO A 708 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 708 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 708 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1195 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 2
        2.09 -     2.79: 1688
        2.79 -     3.49: 10045
        3.49 -     4.20: 15255
        4.20 -     4.90: 26734
  Nonbonded interactions: 53724
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 163 "
            pdb=" O   SER A 679 "
     model   vdw
     1.387 3.120
  nonbonded pdb=" O   TYR A 647 "
            pdb=" OG1 THR A 651 "
     model   vdw
     2.044 3.040
  nonbonded pdb=" O   PHE A 268 "
            pdb=" NE2 GLN A 270 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" OG1 THR C 163 "
            pdb=" OE2 GLU C 209 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" CD2 HIS A 235 "
            pdb="ZN    ZN A 902 "
     model   vdw
     2.168 1.960
  ... (remaining 53719 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ 
r name CB or name CG or name CD or name CE )) or resid 4 through 67 or (resid 68 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 69 or resid 7 \ 
3 through 74 or (resid 75 and (name N or name CA or name C or name O or name CB  \ 
or name CG )) or (resid 76 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 77 through 102 or (resid 103 and (name N or name CA or name C or na \ 
me O or name CB or name CG )) or resid 104 through 138 or (resid 139 and (name N \ 
 or name CA or name C or name O or name CB or name CG )) or resid 140 through 15 \ 
7 or (resid 158 and (name N or name CA or name C or name O or name CB or name CG \ 
 or name CD or name CE )) or resid 159 through 230))
  selection = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ 
r name O or name CB or name CG )) or resid 6 through 102 or (resid 103 and (name \ 
 N or name CA or name C or name O or name CB or name CG )) or resid 104 through  \ 
133 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 138 through 156 or (resid 157 through 158 and (name N or name CA or name C o \ 
r name O or name CB or name CG or name CD or name CE )) or resid 159 through 207 \ 
 or (resid 208 through 209 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 210 through 211 or (resid 212 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 213 through 229 or (resid 230 and (name N or name C \ 
A or name C or name O or name CB ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.400
  Find NCS groups from input model:        0.190
  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:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6961  Z= 0.163
  Angle     :  0.592   6.843   9385  Z= 0.353
  Chirality :  0.039   0.224   1045
  Planarity :  0.004   0.055   1198
  Dihedral  : 15.258  89.694   2612
  Min Nonbonded Distance : 1.387

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.27 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.28), residues: 833
  helix: -0.73 (0.24), residues: 457
  sheet: -3.50 (1.08), residues: 18
  loop : -2.92 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 228 
 HIS   0.007   0.001   HIS A 542 
 PHE   0.022   0.002   PHE B 117 
 TYR   0.021   0.002   TYR A 266 
 ARG   0.004   0.000   ARG A 252 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 LEU cc_start: 0.8438 (mt) cc_final: 0.8101 (mt)
REVERT: A  254 LEU cc_start: 0.6824 (tp) cc_final: 0.6526 (tp)
REVERT: C  160 MET cc_start: 0.6214 (tpt) cc_final: 0.5870 (tpt)
  outliers start: 3
  outliers final: 1
  residues processed: 166
  average time/residue: 0.1807
  time to fit residues: 40.1100
Evaluate side-chains
  125 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 GLN
A 585 HIS
C  42 ASN
** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6961  Z= 0.190
  Angle     :  0.636   8.084   9385  Z= 0.340
  Chirality :  0.042   0.143   1045
  Planarity :  0.005   0.055   1198
  Dihedral  :  5.487  45.193    938
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  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: -1.49 (0.28), residues: 833
  helix:  0.27 (0.23), residues: 464
  sheet: -3.19 (0.83), residues: 28
  loop : -2.62 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 228 
 HIS   0.008   0.002   HIS A 235 
 PHE   0.026   0.002   PHE B 174 
 TYR   0.025   0.002   TYR C 125 
 ARG   0.005   0.001   ARG A 506 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  190 LEU cc_start: 0.8177 (mt) cc_final: 0.7700 (mt)
REVERT: A  254 LEU cc_start: 0.6793 (tp) cc_final: 0.6511 (tp)
REVERT: A  564 MET cc_start: 0.7350 (ttm) cc_final: 0.7030 (mtt)
REVERT: B  155 ILE cc_start: 0.7958 (tp) cc_final: 0.7606 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1790
  time to fit residues: 36.2252
Evaluate side-chains
  115 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 68 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 ASN
B 108 ASN
B 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6961  Z= 0.221
  Angle     :  0.641   9.666   9385  Z= 0.334
  Chirality :  0.042   0.151   1045
  Planarity :  0.005   0.055   1198
  Dihedral  :  5.493  42.258    938
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.28), residues: 833
  helix:  0.34 (0.23), residues: 467
  sheet: -3.16 (0.79), residues: 28
  loop : -2.57 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.045   0.003   PHE C 174 
 TYR   0.021   0.002   TYR C 125 
 ARG   0.006   0.001   ARG B 127 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 LEU cc_start: 0.8132 (mt) cc_final: 0.7703 (mt)
REVERT: A  689 MET cc_start: 0.6235 (ttm) cc_final: 0.6015 (ttm)
REVERT: C   56 ARG cc_start: 0.7159 (mtp180) cc_final: 0.6957 (mtp-110)
REVERT: B   59 TRP cc_start: 0.6010 (t60) cc_final: 0.5726 (t60)
REVERT: B  149 TYR cc_start: 0.7063 (m-80) cc_final: 0.6442 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1822
  time to fit residues: 37.2610
Evaluate side-chains
  110 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 76 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 HIS
A 494 GLN
C  42 ASN
** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 GLN
B 224 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6403
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6961  Z= 0.195
  Angle     :  0.607  10.126   9385  Z= 0.318
  Chirality :  0.041   0.146   1045
  Planarity :  0.004   0.054   1198
  Dihedral  :  5.331  39.791    938
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.29), residues: 833
  helix:  0.56 (0.23), residues: 465
  sheet: -3.17 (0.79), residues: 28
  loop : -2.43 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  59 
 HIS   0.007   0.001   HIS A 477 
 PHE   0.054   0.003   PHE C 174 
 TYR   0.015   0.002   TYR A 640 
 ARG   0.004   0.000   ARG A 506 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 LEU cc_start: 0.8059 (mt) cc_final: 0.7614 (mt)
REVERT: A  484 MET cc_start: 0.5191 (mtt) cc_final: 0.4941 (mmm)
REVERT: A  636 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8164 (mm-40)
REVERT: B   59 TRP cc_start: 0.5993 (t60) cc_final: 0.5787 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1920
  time to fit residues: 37.4778
Evaluate side-chains
  114 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 1 optimal weight:   30.0000
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 GLN
C  42 ASN
B 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6961  Z= 0.255
  Angle     :  0.654  11.194   9385  Z= 0.339
  Chirality :  0.042   0.158   1045
  Planarity :  0.005   0.054   1198
  Dihedral  :  5.550  42.638    938
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  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: -1.08 (0.29), residues: 833
  helix:  0.55 (0.24), residues: 467
  sheet: -2.78 (0.84), residues: 28
  loop : -2.41 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.051   0.003   PHE C 174 
 TYR   0.021   0.002   TYR B 211 
 ARG   0.006   0.001   ARG A 506 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.5632 (mmt) cc_final: 0.5413 (mmm)
REVERT: A  636 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8090 (mm-40)
REVERT: B   59 TRP cc_start: 0.6041 (t60) cc_final: 0.5793 (t60)
REVERT: B  149 TYR cc_start: 0.7022 (m-80) cc_final: 0.6441 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2001
  time to fit residues: 37.5713
Evaluate side-chains
  108 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 494 GLN
C  42 ASN
B 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6961  Z= 0.235
  Angle     :  0.661  11.314   9385  Z= 0.342
  Chirality :  0.042   0.177   1045
  Planarity :  0.005   0.056   1198
  Dihedral  :  5.540  40.921    938
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.02 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.29), residues: 833
  helix:  0.54 (0.24), residues: 467
  sheet: -2.48 (0.90), residues: 28
  loop : -2.36 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  59 
 HIS   0.007   0.001   HIS A 568 
 PHE   0.049   0.002   PHE C 174 
 TYR   0.021   0.002   TYR B 211 
 ARG   0.004   0.000   ARG A 506 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  636 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8070 (mm-40)
REVERT: B   59 TRP cc_start: 0.6058 (t60) cc_final: 0.5745 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1788
  time to fit residues: 36.1378
Evaluate side-chains
  112 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 59 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 GLN
C  42 ASN
B 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6353
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6961  Z= 0.175
  Angle     :  0.617  11.084   9385  Z= 0.318
  Chirality :  0.040   0.164   1045
  Planarity :  0.004   0.055   1198
  Dihedral  :  5.208  39.978    938
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.23 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.29), residues: 833
  helix:  0.83 (0.24), residues: 466
  sheet: -2.22 (0.85), residues: 28
  loop : -2.27 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  59 
 HIS   0.005   0.001   HIS A 370 
 PHE   0.046   0.002   PHE C 174 
 TYR   0.024   0.002   TYR C  19 
 ARG   0.005   0.000   ARG C  56 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  636 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8068 (mm-40)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1828
  time to fit residues: 35.8146
Evaluate side-chains
  110 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
A 494 GLN
** C  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6961  Z= 0.350
  Angle     :  0.781  16.746   9385  Z= 0.395
  Chirality :  0.045   0.191   1045
  Planarity :  0.006   0.068   1198
  Dihedral  :  6.059  45.645    938
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.92 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.29), residues: 833
  helix:  0.29 (0.23), residues: 470
  sheet: -2.29 (1.06), residues: 17
  loop : -2.30 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  59 
 HIS   0.011   0.002   HIS A 568 
 PHE   0.045   0.003   PHE C 174 
 TYR   0.019   0.002   TYR C 125 
 ARG   0.006   0.001   ARG B  41 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  126 TYR cc_start: 0.8102 (m-10) cc_final: 0.7453 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1805
  time to fit residues: 36.2108
Evaluate side-chains
  118 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   chunk 71 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 GLN
C  42 ASN
** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 GLN
B 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6395
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6961  Z= 0.203
  Angle     :  0.671  12.221   9385  Z= 0.344
  Chirality :  0.042   0.205   1045
  Planarity :  0.004   0.055   1198
  Dihedral  :  5.510  40.581    938
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.27 %
    Favored  : 99.59 %
  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: -0.84 (0.29), residues: 833
  helix:  0.72 (0.24), residues: 467
  sheet: -2.35 (0.88), residues: 28
  loop : -2.29 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  59 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.041   0.002   PHE C 174 
 TYR   0.031   0.002   TYR B 178 
 ARG   0.007   0.001   ARG B  41 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   83 ARG cc_start: 0.6579 (ttp-110) cc_final: 0.5828 (ttp80)
REVERT: B  126 TYR cc_start: 0.7951 (m-10) cc_final: 0.7435 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1953
  time to fit residues: 39.3074
Evaluate side-chains
  122 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0470
   chunk 51 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
A 494 GLN
C  42 ASN
** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6376
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6961  Z= 0.188
  Angle     :  0.642   9.769   9385  Z= 0.329
  Chirality :  0.042   0.194   1045
  Planarity :  0.004   0.055   1198
  Dihedral  :  5.325  41.112    938
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.14 %
    Favored  : 99.59 %
  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: -0.68 (0.29), residues: 833
  helix:  0.87 (0.24), residues: 466
  sheet: -2.42 (0.85), residues: 28
  loop : -2.22 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  59 
 HIS   0.006   0.001   HIS A 370 
 PHE   0.040   0.002   PHE C 174 
 TYR   0.027   0.002   TYR C 125 
 ARG   0.006   0.000   ARG B  41 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   83 ARG cc_start: 0.6535 (ttp-110) cc_final: 0.5705 (ttp80)
REVERT: B  126 TYR cc_start: 0.7972 (m-10) cc_final: 0.7129 (m-80)
REVERT: B  131 GLU cc_start: 0.7034 (pp20) cc_final: 0.6827 (pt0)
REVERT: B  160 MET cc_start: 0.5167 (mmm) cc_final: 0.4963 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 152
  average time/residue: 0.1985
  time to fit residues: 39.5893
Evaluate side-chains
  120 residues out of total 755 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 GLN
** C  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 GLN
B 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.174530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.153948 restraints weight = 10067.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.154408 restraints weight = 7882.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.156066 restraints weight = 7762.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6961  Z= 0.317
  Angle     :  0.752   9.219   9385  Z= 0.387
  Chirality :  0.045   0.202   1045
  Planarity :  0.005   0.063   1198
  Dihedral  :  5.958  44.403    938
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.29), residues: 833
  helix:  0.38 (0.23), residues: 469
  sheet: -2.52 (0.99), residues: 17
  loop : -2.26 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  59 
 HIS   0.009   0.001   HIS A 568 
 PHE   0.041   0.003   PHE C 174 
 TYR   0.028   0.003   TYR A 640 
 ARG   0.006   0.001   ARG B  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1445.13 seconds
wall clock time: 26 minutes 59.41 seconds (1619.41 seconds total)