Starting phenix.real_space_refine
on Wed Sep 17 17:49:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6f07_4163/09_2025/6f07_4163.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6f07_4163/09_2025/6f07_4163.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6f07_4163/09_2025/6f07_4163.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6f07_4163/09_2025/6f07_4163.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6f07_4163/09_2025/6f07_4163.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6f07_4163/09_2025/6f07_4163.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      54      5.16       5
     C    6551      2.51       5
     N    1670      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10149
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 510, 4249
          Classifications: {'peptide': 510}
          Link IDs: {'PTRANS': 16, 'TRANS': 493}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4746
          Classifications: {'peptide': 575}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 555}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1152
          Classifications: {'peptide': 142}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 132}
          Chain breaks: 2
    Chain: "B"
      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   4346  SG  CYS B  14      22.504  74.855  65.425  1.00228.19           S
  ATOM   4425  SG  CYS B  24      25.564  72.810  64.715  1.00223.95           S
  ATOM   4346  SG  CYS B  14      22.504  74.855  65.425  1.00228.19           S
  ATOM   4473  SG  CYS B  30      25.268  77.024  64.816  1.00203.85           S
  ATOM   4491  SG  CYS B  33      22.225  78.973  63.646  1.00205.77           S
  ATOM   4564  SG  CYS B  42      22.697  77.660  67.746  1.00216.67           S

  Time building chain proxies: 2.80, per 1000 atoms: 0.28
  Number of scatterers: 10149
  At special positions: 0
  Unit cell: (119.658, 112.112, 120.736, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      54     16.00
     O    1872      8.00
     N    1670      7.00
     C    6551      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  99 " - pdb=" SG  CYS B 215 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 408.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B  14 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B  24 "
      pdb="  ZN B 702 "
        pdb="ZN    ZN B 702 " - pdb=" SG  CYS B  33 "
        pdb="ZN    ZN B 702 " - pdb=" SG  CYS B  42 "
        pdb="ZN    ZN B 702 " - pdb=" SG  CYS B  14 "
        pdb="ZN    ZN B 702 " - pdb=" SG  CYS B  30 "
      Number of angles added : 6


  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2386

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      73.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 73
      removed outlier: 3.613A  pdb=" N   GLN A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ASN A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 105
    Processing helix  chain 'A' and resid 107 through 122
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.877A  pdb=" N   TYR A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 146
      removed outlier: 4.095A  pdb=" N   ARG A 139 " --> pdb=" O   GLU A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 173
    Processing helix  chain 'A' and resid 175 through 183
    Processing helix  chain 'A' and resid 185 through 192
    Processing helix  chain 'A' and resid 203 through 223
    Processing helix  chain 'A' and resid 231 through 241
    Processing helix  chain 'A' and resid 242 through 243
      No H-bonds generated for 'chain 'A' and resid 242 through 243'
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.542A  pdb=" N   ASP A 248 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 266
    Processing helix  chain 'A' and resid 279 through 302
      removed outlier: 3.529A  pdb=" N   SER A 283 " --> pdb=" O   ASP A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 357
    Processing helix  chain 'A' and resid 366 through 386
    Processing helix  chain 'A' and resid 393 through 422
    Processing helix  chain 'A' and resid 426 through 444
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 451 through 455
    Processing helix  chain 'A' and resid 456 through 477
      removed outlier: 4.079A  pdb=" N   MET A 460 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE A 476 " --> pdb=" O   PHE A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 494
      removed outlier: 3.819A  pdb=" N   ALA A 494 " --> pdb=" O   THR A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 496
      No H-bonds generated for 'chain 'A' and resid 495 through 496'
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 500 through 523
      removed outlier: 3.640A  pdb=" N   LEU A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TRP A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 552
      removed outlier: 3.758A  pdb=" N   LYS A 539 " --> pdb=" O   HIS A 535 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 563
      removed outlier: 3.859A  pdb=" N   GLY A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 601
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.524A  pdb=" N   LEU A 607 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 20
      removed outlier: 3.509A  pdb=" N   ARG B  20 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 37
    Processing helix  chain 'B' and resid 38 through 44
      removed outlier: 3.732A  pdb=" N   CYS B  42 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 72
      removed outlier: 3.682A  pdb=" N   LEU B  61 " --> pdb=" O   TYR B  57 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ASN B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 79
      removed outlier: 3.813A  pdb=" N   TYR B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 105
    Processing helix  chain 'B' and resid 107 through 122
    Processing helix  chain 'B' and resid 122 through 127
      removed outlier: 3.887A  pdb=" N   TYR B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 146
      removed outlier: 4.055A  pdb=" N   LEU B 138 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ARG B 139 " --> pdb=" O   GLU B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 173
    Processing helix  chain 'B' and resid 175 through 183
    Processing helix  chain 'B' and resid 185 through 192
      removed outlier: 3.723A  pdb=" N   HIS B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 202
    Processing helix  chain 'B' and resid 203 through 223
      removed outlier: 3.531A  pdb=" N   VAL B 207 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 228
      removed outlier: 3.696A  pdb=" N   HIS B 228 " --> pdb=" O   PHE B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 241
      removed outlier: 4.437A  pdb=" N   VAL B 234 " --> pdb=" O   ASP B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 249
      removed outlier: 4.015A  pdb=" N   GLU B 249 " --> pdb=" O   PHE B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 266
    Processing helix  chain 'B' and resid 279 through 302
    Processing helix  chain 'B' and resid 341 through 357
      removed outlier: 3.791A  pdb=" N   ILE B 348 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 386
      removed outlier: 3.751A  pdb=" N   LEU B 370 " --> pdb=" O   PRO B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 422
    Processing helix  chain 'B' and resid 426 through 444
    Processing helix  chain 'B' and resid 451 through 455
    Processing helix  chain 'B' and resid 456 through 477
      removed outlier: 3.973A  pdb=" N   MET B 460 " --> pdb=" O   HIS B 456 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   PHE B 476 " --> pdb=" O   PHE B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 494
    Processing helix  chain 'B' and resid 495 through 496
      No H-bonds generated for 'chain 'B' and resid 495 through 496'
    Processing helix  chain 'B' and resid 497 through 499
      No H-bonds generated for 'chain 'B' and resid 497 through 499'
    Processing helix  chain 'B' and resid 500 through 523
      removed outlier: 3.546A  pdb=" N   LEU B 504 " --> pdb=" O   PHE B 500 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP B 505 " --> pdb=" O   GLY B 501 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU B 519 " --> pdb=" O   SER B 515 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   TRP B 521 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 552
      removed outlier: 3.663A  pdb=" N   LYS B 539 " --> pdb=" O   HIS B 535 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE B 545 " --> pdb=" O   LEU B 541 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   LYS B 546 " --> pdb=" O   GLN B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 563
      removed outlier: 3.948A  pdb=" N   GLY B 563 " --> pdb=" O   ILE B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 601
    Processing helix  chain 'B' and resid 602 through 606
      removed outlier: 3.937A  pdb=" N   ASP B 605 " --> pdb=" O   ASN B 602 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 24
    Processing helix  chain 'D' and resid 26 through 34
    Processing helix  chain 'D' and resid 83 through 97
    Processing helix  chain 'D' and resid 107 through 112
    Processing helix  chain 'D' and resid 117 through 124
    Processing helix  chain 'D' and resid 127 through 142
    Processing helix  chain 'D' and resid 143 through 159
    Processing helix  chain 'D' and resid 177 through 187
      removed outlier: 3.608A  pdb=" N   ALA D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA D 183 " --> pdb=" O   GLU D 179 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 183 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528
      removed outlier: 4.126A  pdb=" N   TYR A 534 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 18
      removed outlier: 6.459A  pdb=" N   VAL D   7 " --> pdb=" O   MET D  77 " (cutoff:3.500A)

    596 hydrogen bonds defined for protein.
    1755 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: 1.42 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: 3061
        1.34 -     1.46: 2009
        1.46 -     1.58: 5223
        1.58 -     1.69: 0
        1.69 -     1.81: 85
  Bond restraints: 10378
  Sorted by residual:
  bond pdb=" CA  ASN B 543 "
       pdb=" C   ASN B 543 "
    ideal  model  delta    sigma   weight residual
    1.522  1.502  0.020 1.20e-02 6.94e+03 2.77e+00
  bond pdb=" C   SER B 363 "
       pdb=" N   LYS B 364 "
    ideal  model  delta    sigma   weight residual
    1.331  1.310  0.021 1.36e-02 5.41e+03 2.32e+00
  bond pdb=" N   ASN B 543 "
       pdb=" CA  ASN B 543 "
    ideal  model  delta    sigma   weight residual
    1.460  1.443  0.017 1.14e-02 7.69e+03 2.29e+00
  bond pdb=" C   LEU A  58 "
       pdb=" N   PRO A  59 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.20e-02 6.94e+03 2.20e+00
  bond pdb=" CA  LEU A  58 "
       pdb=" C   LEU A  58 "
    ideal  model  delta    sigma   weight residual
    1.521  1.538 -0.017 1.14e-02 7.69e+03 2.18e+00
  ... (remaining 10373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 13741
        2.73 -     5.46: 261
        5.46 -     8.19: 31
        8.19 -    10.92: 4
       10.92 -    13.66: 1
  Bond angle restraints: 14038
  Sorted by residual:
  angle pdb=" N   ASN B 543 "
        pdb=" CA  ASN B 543 "
        pdb=" C   ASN B 543 "
      ideal   model   delta    sigma   weight residual
     114.62  100.96   13.66 1.14e+00 7.69e-01 1.43e+02
  angle pdb=" N   VAL A 185 "
        pdb=" CA  VAL A 185 "
        pdb=" C   VAL A 185 "
      ideal   model   delta    sigma   weight residual
     113.53  107.58    5.95 9.80e-01 1.04e+00 3.68e+01
  angle pdb=" N   THR B   6 "
        pdb=" CA  THR B   6 "
        pdb=" C   THR B   6 "
      ideal   model   delta    sigma   weight residual
     108.76  116.77   -8.01 1.58e+00 4.01e-01 2.57e+01
  angle pdb=" N   GLU A 338 "
        pdb=" CA  GLU A 338 "
        pdb=" C   GLU A 338 "
      ideal   model   delta    sigma   weight residual
     114.56  108.84    5.72 1.27e+00 6.20e-01 2.03e+01
  angle pdb=" C   VAL B 185 "
        pdb=" N   TYR B 186 "
        pdb=" CA  TYR B 186 "
      ideal   model   delta    sigma   weight residual
     120.09  125.49   -5.40 1.25e+00 6.40e-01 1.87e+01
  ... (remaining 14033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 5875
       15.42 -    30.84: 300
       30.84 -    46.27: 62
       46.27 -    61.69: 7
       61.69 -    77.11: 8
  Dihedral angle restraints: 6252
    sinusoidal: 2588
      harmonic: 3664
  Sorted by residual:
  dihedral pdb=" CA  LEU B 312 "
           pdb=" C   LEU B 312 "
           pdb=" N   HIS B 313 "
           pdb=" CA  HIS B 313 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.37   37.63     0      5.00e+00 4.00e-02 5.66e+01
  dihedral pdb=" CA  LEU B   8 "
           pdb=" C   LEU B   8 "
           pdb=" N   LYS B   9 "
           pdb=" CA  LYS B   9 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.13  -30.87     0      5.00e+00 4.00e-02 3.81e+01
  dihedral pdb=" CA  MET B  27 "
           pdb=" C   MET B  27 "
           pdb=" N   ILE B  28 "
           pdb=" CA  ILE B  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.17  -26.83     0      5.00e+00 4.00e-02 2.88e+01
  ... (remaining 6249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 993
       0.046 -    0.092: 431
       0.092 -    0.138: 115
       0.138 -    0.184: 14
       0.184 -    0.230: 3
  Chirality restraints: 1556
  Sorted by residual:
  chirality pdb=" CA  ASN B 543 "
            pdb=" N   ASN B 543 "
            pdb=" C   ASN B 543 "
            pdb=" CB  ASN B 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  ILE B  28 "
            pdb=" CA  ILE B  28 "
            pdb=" CG1 ILE B  28 "
            pdb=" CG2 ILE B  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  VAL B 459 "
            pdb=" CA  VAL B 459 "
            pdb=" CG1 VAL B 459 "
            pdb=" CG2 VAL B 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1553 not shown)

  Planarity restraints: 1769
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 245 "    0.053 5.00e-02 4.00e+02   7.95e-02 1.01e+01
        pdb=" N   PRO A 246 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 245 "   -0.047 5.00e-02 4.00e+02   7.05e-02 7.96e+00
        pdb=" N   PRO B 246 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO B 246 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 246 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 508 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.44e+00
        pdb=" C   VAL B 508 "    0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 508 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TYR B 509 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1766 not shown)

  Histogram of nonbonded interaction distances:
        0.71 -     1.55: 9
        1.55 -     2.38: 39
        2.38 -     3.22: 9695
        3.22 -     4.06: 24077
        4.06 -     4.90: 43465
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 77285
  Sorted by model distance:
  nonbonded pdb=" CB  HIS B  12 "
            pdb=" CG  PHE D 176 "
     model   vdw
     0.707 3.660
  nonbonded pdb=" CG  HIS B  12 "
            pdb=" CG  PHE D 176 "
     model   vdw
     0.866 3.480
  nonbonded pdb=" CB  HIS B  12 "
            pdb=" CD2 PHE D 176 "
     model   vdw
     1.161 3.740
  nonbonded pdb=" CG  HIS B  12 "
            pdb=" CD1 PHE D 176 "
     model   vdw
     1.165 3.560
  nonbonded pdb=" CD2 HIS B  12 "
            pdb=" CA  PHE D 176 "
     model   vdw
     1.174 3.690
  ... (remaining 77280 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 'A'
  selection = (chain 'B' and (resid 55 through 313 or resid 336 through 565 or resid 588 throu \ 
gh 608))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.310
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.350
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5565
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      :  0.008   0.159  10386  Z= 0.359
  Angle     :  1.004  22.350  14046  Z= 0.568
  Chirality :  0.053   0.230   1556
  Planarity :  0.008   0.079   1769
  Dihedral  : 10.285  77.111   3863
  Min Nonbonded Distance : 0.707

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.12 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  1.93 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.04 (0.19), residues: 1209
  helix: -1.48 (0.14), residues: 817
  sheet:  0.48 (1.77), residues: 14
  loop : -3.08 (0.26), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  20 
 TYR   0.027   0.002   TYR B 382 
 PHE   0.040   0.003   PHE D 176 
 TRP   0.037   0.004   TRP A  65 
 HIS   0.008   0.002   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 (10378)
  covalent geometry    : angle       0.95809 (14038)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       2.25148 (    2)
  hydrogen bonds       : bond        0.15065 (  596)
  hydrogen bonds       : angle       6.13579 ( 1755)
  metal coordination   : bond        0.13637 (    6)
  metal coordination   : angle      14.44752 (    6)
  Misc. bond           : bond        0.15934 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 300
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 HIS cc_start: 0.6376 (m-70) cc_final: 0.6138 (m90)
REVERT: A  199 ASN cc_start: 0.8173 (m-40) cc_final: 0.7772 (m-40)
REVERT: A  200 TRP cc_start: 0.4857 (m100) cc_final: 0.4069 (m100)
REVERT: A  255 SER cc_start: 0.7910 (m) cc_final: 0.7503 (t)
REVERT: A  376 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7943 (tp30)
REVERT: A  377 LEU cc_start: 0.7665 (tp) cc_final: 0.7381 (mt)
REVERT: A  387 LEU cc_start: 0.7712 (mt) cc_final: 0.7223 (mp)
REVERT: A  399 GLN cc_start: 0.8380 (tt0) cc_final: 0.8070 (tm-30)
REVERT: A  436 LYS cc_start: 0.8667 (mttm) cc_final: 0.8323 (mmmt)
REVERT: A  473 TYR cc_start: 0.6980 (t80) cc_final: 0.6458 (t80)
REVERT: A  517 LEU cc_start: 0.7584 (tp) cc_final: 0.7064 (mt)
REVERT: A  560 LYS cc_start: 0.7862 (mttt) cc_final: 0.7000 (ttpt)
REVERT: B   38 GLN cc_start: 0.7797 (mt0) cc_final: 0.7547 (mt0)
REVERT: B   43 MET cc_start: 0.7752 (mmm) cc_final: 0.7316 (tpt)
REVERT: B  377 LEU cc_start: 0.6708 (tp) cc_final: 0.6332 (mt)
REVERT: B  378 ASP cc_start: 0.5908 (m-30) cc_final: 0.5575 (m-30)
REVERT: D  127 ASP cc_start: 0.6904 (p0) cc_final: 0.6004 (t0)
REVERT: D  159 ARG cc_start: 0.4592 (mtt90) cc_final: 0.4037 (tpp-160)
  outliers start: 8
  outliers final: 1
  residues processed: 306
  average time/residue: 0.1396
  time to fit residues: 56.4298
Evaluate side-chains
  158 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  67 ASN
A 189 HIS
A 394 ASN
A 399 GLN
A 461 GLN
A 474 GLN
A 543 ASN
B  66 GLN
B  67 ASN
B 228 HIS
B 303 GLN
B 406 GLN
B 445 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.182861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.161806 restraints weight = 17019.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.164777 restraints weight = 10420.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.166732 restraints weight = 7512.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.168051 restraints weight = 6024.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.168564 restraints weight = 5181.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6686
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10386  Z= 0.156
  Angle     :  0.643  10.689  14046  Z= 0.336
  Chirality :  0.040   0.206   1556
  Planarity :  0.006   0.073   1769
  Dihedral  :  5.102  29.880   1341
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  8.93 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.23), residues: 1209
  helix:  0.29 (0.17), residues: 844
  sheet:  0.14 (1.75), residues: 14
  loop : -2.47 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 186 
 TYR   0.021   0.002   TYR A 126 
 PHE   0.023   0.002   PHE D 176 
 TRP   0.034   0.002   TRP A 412 
 HIS   0.023   0.002   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10378)
  covalent geometry    : angle       0.63017 (14038)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       1.43483 (    2)
  hydrogen bonds       : bond        0.05241 (  596)
  hydrogen bonds       : angle       4.46401 ( 1755)
  metal coordination   : bond        0.00593 (    6)
  metal coordination   : angle       6.08967 (    6)
  Misc. bond           : bond        0.01052 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 LEU cc_start: 0.8342 (tp) cc_final: 0.8092 (mt)
REVERT: B    9 LYS cc_start: 0.7585 (mtmm) cc_final: 0.6889 (tttp)
REVERT: B   11 LYS cc_start: 0.5599 (pttt) cc_final: 0.4921 (ptpt)
REVERT: B  314 THR cc_start: 0.6135 (OUTLIER) cc_final: 0.5917 (m)
REVERT: B  591 ARG cc_start: 0.6554 (ttm-80) cc_final: 0.6291 (ttp-170)
REVERT: D   21 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7958 (mmtm)
REVERT: D   30 LYS cc_start: 0.7914 (tptp) cc_final: 0.7677 (tptp)
REVERT: D   34 ASN cc_start: 0.5990 (p0) cc_final: 0.5207 (p0)
REVERT: D  127 ASP cc_start: 0.5459 (p0) cc_final: 0.5119 (t0)
REVERT: D  134 ILE cc_start: 0.6760 (mt) cc_final: 0.6513 (mt)
  outliers start: 30
  outliers final: 18
  residues processed: 205
  average time/residue: 0.1198
  time to fit residues: 33.6363
Evaluate side-chains
  143 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  512 GLU
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain D residue   17 THR
Chi-restraints excluded: chain D residue   33 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0670
   chunk 53 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 78 optimal weight:    0.1980
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 GLN
B 433 HIS
B 444 ASN
** D  34 ASN ** 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 = 0.4376 r_free = 0.4376 target = 0.184503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.163853 restraints weight = 16928.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.166875 restraints weight = 10178.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.168854 restraints weight = 7253.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.170219 restraints weight = 5810.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.171123 restraints weight = 4954.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10386  Z= 0.115
  Angle     :  0.541   8.500  14046  Z= 0.282
  Chirality :  0.038   0.162   1556
  Planarity :  0.005   0.053   1769
  Dihedral  :  4.549  26.481   1340
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.43 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.24), residues: 1209
  helix:  1.00 (0.18), residues: 850
  sheet:  0.22 (1.74), residues: 14
  loop : -2.27 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 121 
 TYR   0.027   0.001   TYR A 126 
 PHE   0.013   0.001   PHE D 102 
 TRP   0.043   0.002   TRP A 412 
 HIS   0.018   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (10378)
  covalent geometry    : angle       0.53277 (14038)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       0.71356 (    2)
  hydrogen bonds       : bond        0.04140 (  596)
  hydrogen bonds       : angle       4.02316 ( 1755)
  metal coordination   : bond        0.00331 (    6)
  metal coordination   : angle       4.68558 (    6)
  Misc. bond           : bond        0.00927 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLN cc_start: 0.5856 (mm-40) cc_final: 0.5643 (mm-40)
REVERT: A  127 PHE cc_start: 0.7395 (t80) cc_final: 0.7079 (t80)
REVERT: A  173 TYR cc_start: 0.5981 (m-80) cc_final: 0.5326 (m-80)
REVERT: A  204 MET cc_start: 0.5915 (mmt) cc_final: 0.5530 (tpp)
REVERT: A  517 LEU cc_start: 0.8251 (tp) cc_final: 0.8024 (tp)
REVERT: B    9 LYS cc_start: 0.7501 (mtmm) cc_final: 0.6809 (tttp)
REVERT: B  417 MET cc_start: 0.7812 (mmt) cc_final: 0.7065 (ttm)
REVERT: B  444 ASN cc_start: 0.7955 (t160) cc_final: 0.7699 (m110)
REVERT: B  603 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5844 (tt)
REVERT: D   34 ASN cc_start: 0.6221 (p0) cc_final: 0.5804 (p0)
REVERT: D   77 MET cc_start: 0.7191 (ttp) cc_final: 0.6193 (ttm)
REVERT: D  127 ASP cc_start: 0.5487 (p0) cc_final: 0.4981 (t0)
REVERT: D  128 GLN cc_start: 0.7034 (tp-100) cc_final: 0.6784 (tp-100)
  outliers start: 23
  outliers final: 14
  residues processed: 177
  average time/residue: 0.1069
  time to fit residues: 27.0896
Evaluate side-chains
  146 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain D residue   17 THR
Chi-restraints excluded: chain D residue  136 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0040
   chunk 51 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 108 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 75 optimal weight:    0.1980
   overall best weight:    1.0398

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.181152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.159959 restraints weight = 16973.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.163034 restraints weight = 10205.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.165034 restraints weight = 7266.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.166407 restraints weight = 5801.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.167092 restraints weight = 4964.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.5139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10386  Z= 0.117
  Angle     :  0.543   7.340  14046  Z= 0.283
  Chirality :  0.038   0.149   1556
  Planarity :  0.004   0.049   1769
  Dihedral  :  4.303  23.654   1340
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.17 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.25), residues: 1209
  helix:  1.38 (0.18), residues: 842
  sheet: -0.03 (1.67), residues: 14
  loop : -2.05 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 121 
 TYR   0.017   0.001   TYR A 509 
 PHE   0.016   0.001   PHE D 102 
 TRP   0.050   0.002   TRP A 412 
 HIS   0.016   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (10378)
  covalent geometry    : angle       0.53590 (14038)
  SS BOND              : bond        0.00296 (    1)
  SS BOND              : angle       0.47876 (    2)
  hydrogen bonds       : bond        0.04165 (  596)
  hydrogen bonds       : angle       3.89154 ( 1755)
  metal coordination   : bond        0.00432 (    6)
  metal coordination   : angle       4.25665 (    6)
  Misc. bond           : bond        0.00700 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 158
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.6822 (m-10) cc_final: 0.6435 (m-10)
REVERT: A  152 HIS cc_start: 0.3544 (OUTLIER) cc_final: 0.3205 (m90)
REVERT: A  173 TYR cc_start: 0.5929 (m-80) cc_final: 0.5372 (m-80)
REVERT: A  204 MET cc_start: 0.5902 (mmt) cc_final: 0.5519 (tpp)
REVERT: A  300 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7846 (t0)
REVERT: B    9 LYS cc_start: 0.7623 (mtmm) cc_final: 0.6857 (tttp)
REVERT: B   43 MET cc_start: 0.6940 (tpt) cc_final: 0.6735 (tpt)
REVERT: B  316 VAL cc_start: 0.7016 (OUTLIER) cc_final: 0.6693 (m)
REVERT: B  417 MET cc_start: 0.7687 (mmt) cc_final: 0.7363 (ttt)
REVERT: D   24 GLU cc_start: 0.6610 (tp30) cc_final: 0.6318 (tt0)
REVERT: D   34 ASN cc_start: 0.6395 (p0) cc_final: 0.5927 (p0)
REVERT: D   77 MET cc_start: 0.7396 (ttp) cc_final: 0.6906 (ttm)
REVERT: D  127 ASP cc_start: 0.5679 (p0) cc_final: 0.5021 (t0)
REVERT: D  128 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6870 (tp-100)
  outliers start: 32
  outliers final: 19
  residues processed: 180
  average time/residue: 0.1106
  time to fit residues: 28.0803
Evaluate side-chains
  161 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  458 MET
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain D residue  136 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 108 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.177412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.158199 restraints weight = 17386.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.160813 restraints weight = 11004.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.162617 restraints weight = 8105.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.163783 restraints weight = 6564.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.164276 restraints weight = 5685.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.5810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10386  Z= 0.147
  Angle     :  0.592   7.349  14046  Z= 0.309
  Chirality :  0.040   0.157   1556
  Planarity :  0.004   0.044   1769
  Dihedral  :  4.383  23.220   1340
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.05 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.25), residues: 1209
  helix:  1.45 (0.18), residues: 847
  sheet: -0.43 (1.60), residues: 14
  loop : -2.04 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   4 
 TYR   0.015   0.002   TYR A 158 
 PHE   0.021   0.002   PHE A 183 
 TRP   0.062   0.002   TRP A 412 
 HIS   0.016   0.002   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10378)
  covalent geometry    : angle       0.58661 (14038)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       0.33656 (    2)
  hydrogen bonds       : bond        0.04717 (  596)
  hydrogen bonds       : angle       4.02093 ( 1755)
  metal coordination   : bond        0.00526 (    6)
  metal coordination   : angle       3.92281 (    6)
  Misc. bond           : bond        0.00799 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 153
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5974 (mmt) cc_final: 0.5645 (tpp)
REVERT: A  226 MET cc_start: 0.6996 (mmm) cc_final: 0.6592 (mtp)
REVERT: A  300 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7791 (t0)
REVERT: A  377 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7805 (mt)
REVERT: A  460 MET cc_start: 0.6977 (tmm) cc_final: 0.6678 (tmm)
REVERT: B    9 LYS cc_start: 0.7601 (mtmm) cc_final: 0.6941 (tttp)
REVERT: B  316 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6684 (m)
REVERT: B  376 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6336 (mp0)
REVERT: B  417 MET cc_start: 0.7807 (mmt) cc_final: 0.7433 (ttt)
REVERT: D   21 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7775 (mmtm)
  outliers start: 40
  outliers final: 19
  residues processed: 184
  average time/residue: 0.1086
  time to fit residues: 28.5434
Evaluate side-chains
  153 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  531 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  532 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 101 optimal weight:    0.0030
   chunk 115 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 303 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.180852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.161954 restraints weight = 17473.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.164625 restraints weight = 11006.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.166368 restraints weight = 8045.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.167610 restraints weight = 6509.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.168442 restraints weight = 5592.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6794
moved from start:          0.6077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10386  Z= 0.113
  Angle     :  0.557   9.457  14046  Z= 0.288
  Chirality :  0.039   0.161   1556
  Planarity :  0.004   0.043   1769
  Dihedral  :  4.186  22.612   1340
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.10 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.25), residues: 1209
  helix:  1.60 (0.18), residues: 848
  sheet: -0.14 (1.58), residues: 14
  loop : -1.90 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 375 
 TYR   0.017   0.001   TYR A 143 
 PHE   0.020   0.001   PHE A 476 
 TRP   0.061   0.002   TRP A 412 
 HIS   0.014   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10378)
  covalent geometry    : angle       0.55222 (14038)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       0.18672 (    2)
  hydrogen bonds       : bond        0.03941 (  596)
  hydrogen bonds       : angle       3.89395 ( 1755)
  metal coordination   : bond        0.00331 (    6)
  metal coordination   : angle       3.45843 (    6)
  Misc. bond           : bond        0.00668 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ASN cc_start: 0.5877 (t0) cc_final: 0.5526 (p0)
REVERT: A  204 MET cc_start: 0.5986 (mmt) cc_final: 0.5610 (tpp)
REVERT: A  226 MET cc_start: 0.6970 (mmm) cc_final: 0.6431 (mtp)
REVERT: A  460 MET cc_start: 0.6763 (tmm) cc_final: 0.6544 (tmm)
REVERT: B    9 LYS cc_start: 0.7597 (mtmm) cc_final: 0.6952 (tttp)
REVERT: B  103 MET cc_start: 0.5662 (mpp) cc_final: 0.4708 (mtm)
REVERT: B  316 VAL cc_start: 0.6754 (OUTLIER) cc_final: 0.6460 (m)
REVERT: B  376 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6239 (mp0)
REVERT: D   24 GLU cc_start: 0.6534 (tp30) cc_final: 0.5894 (mt-10)
  outliers start: 26
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1040
  time to fit residues: 24.8031
Evaluate side-chains
  153 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  458 MET
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   35 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 114 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 25 optimal weight:    0.2980
   chunk 100 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.181541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163043 restraints weight = 17167.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.165763 restraints weight = 10770.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.167574 restraints weight = 7824.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.168532 restraints weight = 6281.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.169406 restraints weight = 5483.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.6323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10386  Z= 0.107
  Angle     :  0.535   7.704  14046  Z= 0.276
  Chirality :  0.038   0.136   1556
  Planarity :  0.004   0.042   1769
  Dihedral  :  4.027  24.354   1340
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.62 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.25), residues: 1209
  helix:  1.70 (0.18), residues: 847
  sheet: -0.05 (1.56), residues: 14
  loop : -1.75 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 375 
 TYR   0.013   0.001   TYR B 301 
 PHE   0.024   0.001   PHE A 476 
 TRP   0.064   0.002   TRP A 412 
 HIS   0.014   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10378)
  covalent geometry    : angle       0.53104 (14038)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       0.39961 (    2)
  hydrogen bonds       : bond        0.03676 (  596)
  hydrogen bonds       : angle       3.78315 ( 1755)
  metal coordination   : bond        0.00341 (    6)
  metal coordination   : angle       3.13172 (    6)
  Misc. bond           : bond        0.00651 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ASN cc_start: 0.5972 (t0) cc_final: 0.5648 (p0)
REVERT: A  204 MET cc_start: 0.5954 (mmt) cc_final: 0.5582 (tpp)
REVERT: A  226 MET cc_start: 0.6934 (mmm) cc_final: 0.6344 (mtp)
REVERT: B    9 LYS cc_start: 0.7607 (mtmm) cc_final: 0.6950 (tttp)
REVERT: B  316 VAL cc_start: 0.6889 (OUTLIER) cc_final: 0.6575 (m)
REVERT: B  376 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6413 (mp0)
REVERT: D   34 ASN cc_start: 0.7240 (p0) cc_final: 0.6744 (p0)
  outliers start: 27
  outliers final: 22
  residues processed: 167
  average time/residue: 0.1023
  time to fit residues: 24.7107
Evaluate side-chains
  153 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  531 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  458 MET
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain D residue   35 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 75 optimal weight:    0.1980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN
B  66 GLN
B 445 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.180228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.161567 restraints weight = 17277.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.164248 restraints weight = 10769.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.166032 restraints weight = 7819.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.167237 restraints weight = 6286.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.167775 restraints weight = 5415.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.6530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10386  Z= 0.118
  Angle     :  0.556   8.681  14046  Z= 0.286
  Chirality :  0.039   0.235   1556
  Planarity :  0.004   0.042   1769
  Dihedral  :  4.066  23.110   1340
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.59 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.25), residues: 1209
  helix:  1.68 (0.18), residues: 848
  sheet: -0.05 (1.54), residues: 14
  loop : -1.74 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 375 
 TYR   0.031   0.001   TYR B 601 
 PHE   0.026   0.001   PHE A 476 
 TRP   0.068   0.002   TRP A 412 
 HIS   0.020   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10378)
  covalent geometry    : angle       0.55238 (14038)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       0.38630 (    2)
  hydrogen bonds       : bond        0.03884 (  596)
  hydrogen bonds       : angle       3.83442 ( 1755)
  metal coordination   : bond        0.00391 (    6)
  metal coordination   : angle       3.11855 (    6)
  Misc. bond           : bond        0.00748 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5842 (mmt) cc_final: 0.5597 (tpp)
REVERT: A  226 MET cc_start: 0.6901 (mmm) cc_final: 0.6293 (mtp)
REVERT: A  377 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7784 (mt)
REVERT: A  591 ARG cc_start: 0.6243 (mpt180) cc_final: 0.5949 (mpt180)
REVERT: B    9 LYS cc_start: 0.7675 (mtmm) cc_final: 0.6975 (tttp)
REVERT: B  115 MET cc_start: 0.7678 (mmp) cc_final: 0.7287 (mmp)
REVERT: B  316 VAL cc_start: 0.6914 (OUTLIER) cc_final: 0.6592 (m)
REVERT: B  376 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6539 (mp0)
REVERT: D   34 ASN cc_start: 0.7349 (p0) cc_final: 0.6890 (p0)
  outliers start: 29
  outliers final: 25
  residues processed: 160
  average time/residue: 0.0989
  time to fit residues: 23.2278
Evaluate side-chains
  159 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  531 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  458 MET
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   35 ASP
Chi-restraints excluded: chain D residue   87 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0030
   chunk 116 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 GLN
B 142 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.178901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.160345 restraints weight = 17147.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.163015 restraints weight = 10693.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.164843 restraints weight = 7750.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.166044 restraints weight = 6187.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.166376 restraints weight = 5300.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.6693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10386  Z= 0.119
  Angle     :  0.562  10.992  14046  Z= 0.286
  Chirality :  0.039   0.240   1556
  Planarity :  0.004   0.041   1769
  Dihedral  :  4.071  24.207   1340
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.24 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1209
  helix:  1.65 (0.18), residues: 843
  sheet: -0.12 (1.54), residues: 14
  loop : -1.78 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 375 
 TYR   0.028   0.001   TYR B 601 
 PHE   0.023   0.001   PHE A 476 
 TRP   0.069   0.002   TRP A 412 
 HIS   0.018   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10378)
  covalent geometry    : angle       0.55395 (14038)
  SS BOND              : bond        0.00294 (    1)
  SS BOND              : angle       0.32789 (    2)
  hydrogen bonds       : bond        0.03887 (  596)
  hydrogen bonds       : angle       3.83525 ( 1755)
  metal coordination   : bond        0.00536 (    6)
  metal coordination   : angle       4.71050 (    6)
  Misc. bond           : bond        0.00701 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 VAL cc_start: 0.5809 (OUTLIER) cc_final: 0.5608 (t)
REVERT: A  204 MET cc_start: 0.5739 (mmt) cc_final: 0.5507 (tpp)
REVERT: A  377 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7825 (mt)
REVERT: A  591 ARG cc_start: 0.6312 (mpt180) cc_final: 0.5909 (mpp-170)
REVERT: B    9 LYS cc_start: 0.7564 (mtmm) cc_final: 0.6883 (tttp)
REVERT: B  115 MET cc_start: 0.7681 (mmp) cc_final: 0.7342 (mmp)
REVERT: B  316 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6544 (m)
REVERT: B  489 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8716 (mt)
  outliers start: 29
  outliers final: 23
  residues processed: 159
  average time/residue: 0.0992
  time to fit residues: 23.0664
Evaluate side-chains
  162 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  531 ASP
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  458 MET
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   31 ASN
Chi-restraints excluded: chain D residue   35 ASP
Chi-restraints excluded: chain D residue   87 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 101 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 104 optimal weight:    0.0770
   chunk 29 optimal weight:    0.7980
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.177261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.158514 restraints weight = 17042.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.161144 restraints weight = 10715.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.162922 restraints weight = 7817.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.163839 restraints weight = 6290.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.164754 restraints weight = 5505.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.6853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10386  Z= 0.131
  Angle     :  0.589  10.828  14046  Z= 0.300
  Chirality :  0.040   0.213   1556
  Planarity :  0.004   0.043   1769
  Dihedral  :  4.143  23.762   1340
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.41 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1209
  helix:  1.62 (0.18), residues: 849
  sheet: -0.31 (1.52), residues: 14
  loop : -1.75 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 375 
 TYR   0.022   0.001   TYR A 143 
 PHE   0.024   0.002   PHE A 476 
 TRP   0.077   0.002   TRP A 412 
 HIS   0.016   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10378)
  covalent geometry    : angle       0.58130 (14038)
  SS BOND              : bond        0.00324 (    1)
  SS BOND              : angle       0.22350 (    2)
  hydrogen bonds       : bond        0.04239 (  596)
  hydrogen bonds       : angle       3.89051 ( 1755)
  metal coordination   : bond        0.00545 (    6)
  metal coordination   : angle       4.55670 (    6)
  Misc. bond           : bond        0.00690 (    1)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5733 (mmt) cc_final: 0.5511 (tpp)
REVERT: A  377 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7916 (mt)
REVERT: A  527 LEU cc_start: 0.7645 (tp) cc_final: 0.7359 (tt)
REVERT: A  591 ARG cc_start: 0.6351 (mpt180) cc_final: 0.5939 (mpp-170)
REVERT: B    9 LYS cc_start: 0.7540 (mtmm) cc_final: 0.6879 (tttp)
REVERT: B  115 MET cc_start: 0.7754 (mmp) cc_final: 0.7407 (mmp)
REVERT: B  316 VAL cc_start: 0.6771 (m) cc_final: 0.6387 (m)
REVERT: B  376 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6574 (mp0)
  outliers start: 28
  outliers final: 24
  residues processed: 164
  average time/residue: 0.0990
  time to fit residues: 23.9067
Evaluate side-chains
  159 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  418 TYR
Chi-restraints excluded: chain A residue  531 ASP
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 PHE
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  458 MET
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   35 ASP
Chi-restraints excluded: chain D residue   87 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0970
   chunk 109 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0980
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0980
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.182752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.164409 restraints weight = 17251.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.167200 restraints weight = 10600.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.169022 restraints weight = 7603.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.170232 restraints weight = 6060.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.170871 restraints weight = 5174.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.7036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10386  Z= 0.111
  Angle     :  0.571  12.449  14046  Z= 0.289
  Chirality :  0.039   0.241   1556
  Planarity :  0.004   0.039   1769
  Dihedral  :  3.993  24.836   1340
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.94 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.25), residues: 1209
  helix:  1.75 (0.18), residues: 850
  sheet: -0.07 (1.59), residues: 14
  loop : -1.57 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 375 
 TYR   0.019   0.001   TYR A 143 
 PHE   0.023   0.001   PHE A 476 
 TRP   0.061   0.002   TRP A 412 
 HIS   0.017   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10378)
  covalent geometry    : angle       0.56523 (14038)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       0.13687 (    2)
  hydrogen bonds       : bond        0.03476 (  596)
  hydrogen bonds       : angle       3.75215 ( 1755)
  metal coordination   : bond        0.00319 (    6)
  metal coordination   : angle       3.83298 (    6)
  Misc. bond           : bond        0.00693 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1832.00 seconds
wall clock time: 32 minutes 31.73 seconds (1951.73 seconds total)