Starting phenix.real_space_refine
on Thu Jul 24 22:11:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mfe_23814/07_2025/7mfe_23814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mfe_23814/07_2025/7mfe_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/cci-nas-00/data/ceres_data/7mfe_23814/07_2025/7mfe_23814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mfe_23814/07_2025/7mfe_23814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mfe_23814/07_2025/7mfe_23814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mfe_23814/07_2025/7mfe_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-5711/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: 4.51, per 1000 atoms: 0.66
  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: 1.73
  Conformation dependent library (CDL) restraints added in 950.7 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: 0.63
  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: 1.77

  Time building geometry restraints manager: 2.08 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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.160
  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:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.100
-------------------------------------------------------------------------------
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      :  0.009   0.758   6965  Z= 0.333
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30016 (  364)
  hydrogen bonds       : angle       9.67014 ( 1071)
  metal coordination   : bond        0.37933 (    4)
  covalent geometry    : bond        0.00245 ( 6961)
  covalent geometry    : angle       0.59217 ( 9385)

*********************** 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 to be fit.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 0.826 
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: 0.1871
  time to fit residues: 41.6316
Evaluate side-chains
  125 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.179969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.157505 restraints weight = 9768.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.159128 restraints weight = 7439.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.161329 restraints weight = 6398.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
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   6965  Z= 0.147
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05753 (  364)
  hydrogen bonds       : angle       5.66270 ( 1071)
  metal coordination   : bond        0.01430 (    4)
  covalent geometry    : bond        0.00299 ( 6961)
  covalent geometry    : angle       0.63588 ( 9385)

*********************** 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 to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  190 LEU cc_start: 0.8194 (mt) cc_final: 0.7713 (mt)
REVERT: A  254 LEU cc_start: 0.6778 (tp) cc_final: 0.6487 (tp)
REVERT: A  564 MET cc_start: 0.7285 (ttm) cc_final: 0.6996 (mtt)
REVERT: C  223 ASP cc_start: 0.7231 (p0) cc_final: 0.7024 (p0)
REVERT: B  155 ILE cc_start: 0.8004 (tp) cc_final: 0.7626 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1683
  time to fit residues: 34.4921
Evaluate side-chains
  115 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0000
   chunk 77 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    1.9590

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.177491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.155525 restraints weight = 10000.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.155799 restraints weight = 7824.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.157459 restraints weight = 7336.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6965  Z= 0.165
  Angle     :  0.654   9.882   9385  Z= 0.341
  Chirality :  0.042   0.151   1045
  Planarity :  0.005   0.055   1198
  Dihedral  :  5.578  41.648    938
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.28), residues: 833
  helix:  0.28 (0.23), residues: 467
  sheet: -3.17 (0.79), residues: 28
  loop : -2.59 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.044   0.003   PHE C 174 
 TYR   0.021   0.002   TYR C 125 
 ARG   0.005   0.001   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05266 (  364)
  hydrogen bonds       : angle       5.32099 ( 1071)
  metal coordination   : bond        0.00671 (    4)
  covalent geometry    : bond        0.00362 ( 6961)
  covalent geometry    : angle       0.65441 ( 9385)

*********************** 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
  150 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 LEU cc_start: 0.8192 (mt) cc_final: 0.7740 (mt)
REVERT: A  689 MET cc_start: 0.6280 (ttm) cc_final: 0.6068 (ttm)
REVERT: C  174 PHE cc_start: 0.5929 (t80) cc_final: 0.5727 (t80)
REVERT: C  223 ASP cc_start: 0.7373 (p0) cc_final: 0.7126 (p0)
REVERT: B   59 TRP cc_start: 0.6114 (t60) cc_final: 0.5793 (t60)
REVERT: B  149 TYR cc_start: 0.7208 (m-80) cc_final: 0.6449 (m-80)
REVERT: B  191 LEU cc_start: 0.7043 (mt) cc_final: 0.6839 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1762
  time to fit residues: 35.8534
Evaluate side-chains
  110 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 27 optimal weight:   20.0000
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0870
   chunk 55 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0980
   chunk 47 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    2.0364

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.176893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.156238 restraints weight = 10142.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.157072 restraints weight = 9356.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.158859 restraints weight = 8596.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6965  Z= 0.163
  Angle     :  0.635  10.748   9385  Z= 0.332
  Chirality :  0.041   0.157   1045
  Planarity :  0.005   0.054   1198
  Dihedral  :  5.582  41.706    938
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  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: -1.28 (0.29), residues: 833
  helix:  0.43 (0.23), residues: 465
  sheet: -3.18 (0.81), residues: 28
  loop : -2.50 (0.33), 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   0.044   0.003   PHE B 174 
 TYR   0.017   0.002   TYR A 640 
 ARG   0.006   0.001   ARG C  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04762 (  364)
  hydrogen bonds       : angle       5.16576 ( 1071)
  metal coordination   : bond        0.00715 (    4)
  covalent geometry    : bond        0.00361 ( 6961)
  covalent geometry    : angle       0.63485 ( 9385)

*********************** 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
  150 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.5863 (mmt) cc_final: 0.5627 (mmm)
REVERT: A  636 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8153 (mm-40)
REVERT: C  223 ASP cc_start: 0.7414 (p0) cc_final: 0.7161 (p0)
REVERT: B   41 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6311 (ttt-90)
REVERT: B   59 TRP cc_start: 0.6107 (t60) cc_final: 0.5861 (t60)
REVERT: B  149 TYR cc_start: 0.7049 (m-80) cc_final: 0.6410 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1811
  time to fit residues: 36.4930
Evaluate side-chains
  110 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 4 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0270
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.3844

-------------------------------------------------------------------------------
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 477 HIS
A 494 GLN
A 585 HIS
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.178398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.156678 restraints weight = 9866.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.156981 restraints weight = 9466.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.158432 restraints weight = 7775.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6965  Z= 0.138
  Angle     :  0.616  10.499   9385  Z= 0.320
  Chirality :  0.041   0.163   1045
  Planarity :  0.004   0.056   1198
  Dihedral  :  5.383  41.040    938
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.29), residues: 833
  helix:  0.66 (0.24), residues: 466
  sheet: -2.79 (0.81), residues: 28
  loop : -2.39 (0.33), residues: 339

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   0.051   0.003   PHE C 174 
 TYR   0.022   0.002   TYR B 211 
 ARG   0.005   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04463 (  364)
  hydrogen bonds       : angle       4.95202 ( 1071)
  metal coordination   : bond        0.00432 (    4)
  covalent geometry    : bond        0.00303 ( 6961)
  covalent geometry    : angle       0.61644 ( 9385)

*********************** 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
  150 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.6090 (mmt) cc_final: 0.5848 (mmm)
REVERT: A  636 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8103 (mm-40)
REVERT: A  704 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.8029 (mtt-85)
REVERT: C  116 VAL cc_start: 0.7863 (t) cc_final: 0.7618 (t)
REVERT: C  223 ASP cc_start: 0.7338 (p0) cc_final: 0.7118 (p0)
REVERT: B   41 ARG cc_start: 0.6478 (ttp80) cc_final: 0.6124 (ttt-90)
REVERT: B  149 TYR cc_start: 0.7080 (m-80) cc_final: 0.6398 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1907
  time to fit residues: 37.7091
Evaluate side-chains
  113 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0370
   chunk 54 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.182499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.161851 restraints weight = 9787.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.165560 restraints weight = 9599.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.166913 restraints weight = 6861.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6965  Z= 0.116
  Angle     :  0.584  10.523   9385  Z= 0.303
  Chirality :  0.040   0.160   1045
  Planarity :  0.004   0.054   1198
  Dihedral  :  5.090  39.747    938
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.19 %
    Favored  : 97.67 %
  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:  0.86 (0.24), residues: 466
  sheet: -2.45 (0.84), residues: 28
  loop : -2.30 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  59 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.037   0.002   PHE C 174 
 TYR   0.017   0.002   TYR C 125 
 ARG   0.005   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04214 (  364)
  hydrogen bonds       : angle       4.64331 ( 1071)
  metal coordination   : bond        0.00282 (    4)
  covalent geometry    : bond        0.00243 ( 6961)
  covalent geometry    : angle       0.58366 ( 9385)

*********************** 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
  158 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  223 ASP cc_start: 0.7229 (p0) cc_final: 0.6985 (p0)
REVERT: B   15 GLN cc_start: 0.7328 (pm20) cc_final: 0.7092 (pm20)
REVERT: B   41 ARG cc_start: 0.6490 (ttp80) cc_final: 0.6038 (ttp80)
REVERT: B  149 TYR cc_start: 0.6827 (m-80) cc_final: 0.6590 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1854
  time to fit residues: 39.0348
Evaluate side-chains
  112 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 68 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.178047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.157069 restraints weight = 10022.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.156506 restraints weight = 8176.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.158922 restraints weight = 7995.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6429
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6965  Z= 0.162
  Angle     :  0.661  13.220   9385  Z= 0.341
  Chirality :  0.042   0.170   1045
  Planarity :  0.005   0.054   1198
  Dihedral  :  5.353  42.781    938
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.37 %
    Favored  : 98.35 %
  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: -0.83 (0.29), residues: 833
  helix:  0.74 (0.24), residues: 467
  sheet: -2.30 (0.86), residues: 28
  loop : -2.31 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  59 
 HIS   0.006   0.001   HIS A 568 
 PHE   0.046   0.003   PHE C 174 
 TYR   0.019   0.002   TYR C 125 
 ARG   0.004   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 (  364)
  hydrogen bonds       : angle       4.90357 ( 1071)
  metal coordination   : bond        0.00642 (    4)
  covalent geometry    : bond        0.00365 ( 6961)
  covalent geometry    : angle       0.66074 ( 9385)

*********************** 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
  146 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  223 ASP cc_start: 0.7391 (p0) cc_final: 0.7161 (p0)
REVERT: B   41 ARG cc_start: 0.6570 (ttp80) cc_final: 0.6101 (ttt-90)
REVERT: B  126 TYR cc_start: 0.8125 (m-10) cc_final: 0.7317 (m-80)
REVERT: B  131 GLU cc_start: 0.7127 (pp20) cc_final: 0.6795 (pt0)
REVERT: B  149 TYR cc_start: 0.6995 (m-80) cc_final: 0.6609 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1832
  time to fit residues: 35.8518
Evaluate side-chains
  112 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0470
   chunk 35 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    1.1482

-------------------------------------------------------------------------------
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
A 512 ASN
C  42 ASN
B 224 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.180321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.159305 restraints weight = 9989.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.160048 restraints weight = 7673.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.161405 restraints weight = 7607.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6965  Z= 0.132
  Angle     :  0.625   9.481   9385  Z= 0.325
  Chirality :  0.041   0.201   1045
  Planarity :  0.004   0.054   1198
  Dihedral  :  5.180  39.368    938
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.37 %
    Favored  : 98.35 %
  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: -0.66 (0.29), residues: 833
  helix:  0.86 (0.24), residues: 468
  sheet: -2.25 (0.85), residues: 28
  loop : -2.21 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  59 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.042   0.002   PHE C 174 
 TYR   0.025   0.002   TYR C  19 
 ARG   0.004   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  364)
  hydrogen bonds       : angle       4.71074 ( 1071)
  metal coordination   : bond        0.00371 (    4)
  covalent geometry    : bond        0.00288 ( 6961)
  covalent geometry    : angle       0.62478 ( 9385)

*********************** 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 to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LEU cc_start: 0.6837 (tp) cc_final: 0.6561 (tp)
REVERT: C  223 ASP cc_start: 0.7356 (p0) cc_final: 0.7110 (p0)
REVERT: B   41 ARG cc_start: 0.6548 (ttp80) cc_final: 0.6041 (ttt-90)
REVERT: B  131 GLU cc_start: 0.7116 (pp20) cc_final: 0.6904 (pt0)
REVERT: B  149 TYR cc_start: 0.6923 (m-80) cc_final: 0.6612 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1694
  time to fit residues: 34.3202
Evaluate side-chains
  116 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 512 ASN
C  42 ASN
B 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.181077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.161865 restraints weight = 10072.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.162568 restraints weight = 9024.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.164100 restraints weight = 8335.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6307
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6965  Z= 0.126
  Angle     :  0.624   8.915   9385  Z= 0.321
  Chirality :  0.041   0.183   1045
  Planarity :  0.004   0.053   1198
  Dihedral  :  5.088  39.900    938
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.55 %
    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: -0.51 (0.29), residues: 833
  helix:  0.99 (0.24), residues: 467
  sheet: -2.13 (0.87), residues: 28
  loop : -2.16 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  59 
 HIS   0.006   0.001   HIS A 370 
 PHE   0.044   0.002   PHE C 174 
 TYR   0.029   0.002   TYR B 178 
 ARG   0.004   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  364)
  hydrogen bonds       : angle       4.62224 ( 1071)
  metal coordination   : bond        0.00289 (    4)
  covalent geometry    : bond        0.00272 ( 6961)
  covalent geometry    : angle       0.62384 ( 9385)

*********************** 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
  152 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LEU cc_start: 0.6689 (tp) cc_final: 0.6391 (tp)
REVERT: C  223 ASP cc_start: 0.7314 (p0) cc_final: 0.7073 (p0)
REVERT: B   41 ARG cc_start: 0.6504 (ttp80) cc_final: 0.5928 (ttp80)
REVERT: B  126 TYR cc_start: 0.8012 (m-10) cc_final: 0.7151 (m-80)
REVERT: B  131 GLU cc_start: 0.7084 (pp20) cc_final: 0.6846 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2257
  time to fit residues: 44.4252
Evaluate side-chains
  118 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 28 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
B 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.183437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.162171 restraints weight = 10054.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.162701 restraints weight = 8539.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.164807 restraints weight = 7649.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6294
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6965  Z= 0.119
  Angle     :  0.610   9.159   9385  Z= 0.316
  Chirality :  0.041   0.178   1045
  Planarity :  0.004   0.053   1198
  Dihedral  :  4.970  38.939    938
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.45 %
  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: -0.33 (0.30), residues: 833
  helix:  1.17 (0.24), residues: 467
  sheet: -2.02 (0.89), residues: 28
  loop : -2.13 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  59 
 HIS   0.005   0.001   HIS A 370 
 PHE   0.041   0.002   PHE C 174 
 TYR   0.022   0.002   TYR C 125 
 ARG   0.008   0.000   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  364)
  hydrogen bonds       : angle       4.49894 ( 1071)
  metal coordination   : bond        0.00158 (    4)
  covalent geometry    : bond        0.00250 ( 6961)
  covalent geometry    : angle       0.60988 ( 9385)

********************** 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
  158 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LEU cc_start: 0.6615 (tp) cc_final: 0.6341 (tp)
REVERT: A  370 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5480 (t70)
REVERT: C   83 ARG cc_start: 0.6746 (ttp80) cc_final: 0.5244 (ttp80)
REVERT: C  223 ASP cc_start: 0.7336 (p0) cc_final: 0.7111 (p0)
REVERT: B  126 TYR cc_start: 0.8048 (m-10) cc_final: 0.7229 (m-80)
REVERT: B  149 TYR cc_start: 0.6804 (m-80) cc_final: 0.6575 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2069
  time to fit residues: 42.3956
Evaluate side-chains
  122 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 224 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.183863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.163400 restraints weight = 10123.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.161914 restraints weight = 8117.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.163734 restraints weight = 8076.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6965  Z= 0.122
  Angle     :  0.605   9.198   9385  Z= 0.317
  Chirality :  0.041   0.180   1045
  Planarity :  0.004   0.054   1198
  Dihedral  :  4.945  39.130    938
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.30), residues: 833
  helix:  1.22 (0.24), residues: 470
  sheet: -1.79 (0.93), residues: 28
  loop : -2.10 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  59 
 HIS   0.005   0.001   HIS A 568 
 PHE   0.039   0.002   PHE C 174 
 TYR   0.028   0.002   TYR C 125 
 ARG   0.011   0.001   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  364)
  hydrogen bonds       : angle       4.48040 ( 1071)
  metal coordination   : bond        0.00292 (    4)
  covalent geometry    : bond        0.00262 ( 6961)
  covalent geometry    : angle       0.60502 ( 9385)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2056.34 seconds
wall clock time: 36 minutes 30.37 seconds (2190.37 seconds total)