Starting phenix.real_space_refine
on Thu Feb 13 12:13:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cp6_16778/02_2025/8cp6_16778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cp6_16778/02_2025/8cp6_16778.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cp6_16778/02_2025/8cp6_16778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cp6_16778/02_2025/8cp6_16778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cp6_16778/02_2025/8cp6_16778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cp6_16778/02_2025/8cp6_16778.cif"
  }
  resolution = 2.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.024
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: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    5535      2.51       5
     N    1685      2.21       5
     O    1664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8899
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 121
          Classifications: {'peptide': 18}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'TRANS': 16}
    Chain: "B"
      Number of atoms: 8614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1084, 8614
          Classifications: {'peptide': 1084}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 52, 'TRANS': 1031}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 164
          Classifications: {'peptide': 27}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 5.20, per 1000 atoms: 0.58
  Number of scatterers: 8899
  At special positions: 0
  Unit cell: (79.206, 80.127, 116.967, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O    1664      8.00
     N    1685      7.00
     C    5535      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1998

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 8 sheets defined
      6.0% alpha, 37.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'B' and resid 152 through 156
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.612A  pdb=" N   GLN B 163 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   THR B 164 " --> pdb=" O   ALA B 160 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 159 through 164'
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 360 through 364
      removed outlier: 3.509A  pdb=" N   ARG B 364 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 407
      removed outlier: 4.185A  pdb=" N   GLY B 406 " --> pdb=" O   ASP B 403 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ARG B 407 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 403 through 407'
    Processing helix  chain 'B' and resid 1035 through 1049
    Processing helix  chain 'B' and resid 1053 through 1057
      removed outlier: 3.704A  pdb=" N   VAL B1057 " --> pdb=" O   ALA B1054 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1143 through 1147
    Processing helix  chain 'B' and resid 1154 through 1158
    Processing helix  chain 'C' and resid 1180 through 1186
    Processing helix  chain 'C' and resid 1187 through 1193
      removed outlier: 3.688A  pdb=" N   GLU C1193 " --> pdb=" O   GLY C1189 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 3.586A  pdb=" N   LEU A  34 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLY B 119 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62
      removed outlier: 4.193A  pdb=" N   GLU B  60 " --> pdb=" O   ARG B  76 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   ARG B  76 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86
      removed outlier: 3.639A  pdb=" N   GLY B  89 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 131
      removed outlier: 6.100A  pdb=" N   TYR B 177 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   SER B 193 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   HIS B 179 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 205
      removed outlier: 5.360A  pdb=" N   THR B 212 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER B 221 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY B 243 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLN B 227 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   LEU B 241 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
      removed outlier: 10.022A  pdb=" N   ARG B 240 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
      removed outlier: 8.619A  pdb=" N   PHE B 272 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   PHE B 242 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR B 270 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 268 " --> pdb=" O   VAL B 244 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU B 246 " --> pdb=" O   TRP B 266 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   TRP B 266 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   ILE B 279 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   VAL B 291 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL B 281 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG B 295 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 5.460A  pdb=" N   LEU B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
      removed outlier: 10.654A  pdb=" N   MET B 298 " --> pdb=" O   TRP B 314 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   TRP B 314 " --> pdb=" O   MET B 298 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   VAL B 300 " --> pdb=" O   TYR B 312 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   VAL B 324 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 366 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   TRP B 366 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 9.553A  pdb=" N   ARG B 365 " --> pdb=" O   TYR B 381 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   TYR B 381 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   THR B 367 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   VAL B 388 " --> pdb=" O   ARG B 400 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   VAL B 431 " --> pdb=" O   PHE B 443 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   THR B 452 " --> pdb=" O   TYR B 463 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ARG B 486 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU B 498 " --> pdb=" O   ARG B 486 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLU B 488 " --> pdb=" O   ALA B 496 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ALA B 496 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   VAL B 517 " --> pdb=" O   ARG B 529 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   ILE B 538 " --> pdb=" O   TYR B 550 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ALA B 547 " --> pdb=" O   ASP B 563 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ASP B 563 " --> pdb=" O   ALA B 547 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   SER B 549 " --> pdb=" O   ILE B 561 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE B 561 " --> pdb=" O   SER B 549 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   GLU B 551 " --> pdb=" O   THR B 559 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   THR B 559 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU B 570 " --> pdb=" O   VAL B 582 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL B 582 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   SER B 572 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   ALA B 580 " --> pdb=" O   TYR B 592 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   VAL B 601 " --> pdb=" O   PHE B 613 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU B 623 " --> pdb=" O   ARG B 614 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   VAL B 622 " --> pdb=" O   TYR B 634 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   ILE B 643 " --> pdb=" O   TYR B 655 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   GLU B 652 " --> pdb=" O   VAL B 668 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   VAL B 668 " --> pdb=" O   GLU B 652 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   THR B 654 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   ILE B 666 " --> pdb=" O   THR B 654 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA B 656 " --> pdb=" O   ALA B 664 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ALA B 664 " --> pdb=" O   TYR B 681 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ALA B 690 " --> pdb=" O   TYR B 701 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   ARG B 710 " --> pdb=" O   HIS B 726 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   SER B 723 " --> pdb=" O   TYR B 739 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   TYR B 739 " --> pdb=" O   SER B 723 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   GLU B 725 " --> pdb=" O   SER B 737 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER B 737 " --> pdb=" O   GLU B 725 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER B 727 " --> pdb=" O   GLN B 735 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   GLN B 735 " --> pdb=" O   TRP B 747 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA B 746 " --> pdb=" O   ALA B 758 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ALA B 758 " --> pdb=" O   ALA B 746 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU B 748 " --> pdb=" O   HIS B 756 " (cutoff:3.500A)
      removed outlier: 11.456A  pdb=" N   HIS B 754 " --> pdb=" O   ARG B 769 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   ARG B 769 " --> pdb=" O   HIS B 754 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   HIS B 756 " --> pdb=" O   PHE B 767 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLU B 764 " --> pdb=" O   ALA B 780 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA B 780 " --> pdb=" O   GLU B 764 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B 766 " --> pdb=" O   ARG B 778 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ARG B 778 " --> pdb=" O   ALA B 766 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   GLU B 768 " --> pdb=" O   VAL B 776 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   VAL B 776 " --> pdb=" O   ARG B 794 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   PHE B 790 " --> pdb=" O   ALA B 780 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   THR B 791 " --> pdb=" O   LEU B 807 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LEU B 807 " --> pdb=" O   THR B 791 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLU B 793 " --> pdb=" O   SER B 805 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   SER B 805 " --> pdb=" O   GLU B 793 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   GLN B 795 " --> pdb=" O   GLN B 803 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   GLN B 803 " --> pdb=" O   TYR B 819 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   VAL B 828 " --> pdb=" O   TYR B 840 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ARG B 839 " --> pdb=" O   SER B 851 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER B 851 " --> pdb=" O   ARG B 839 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLU B 841 " --> pdb=" O   LEU B 849 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 862 through 863
      removed outlier: 4.309A  pdb=" N   ARG B 862 " --> pdb=" O   LEU B 870 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 919 through 920
      removed outlier: 4.927A  pdb=" N   VAL B 934 " --> pdb=" O   LEU B 946 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   VAL B 955 " --> pdb=" O   TYR B 971 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   ILE B 980 " --> pdb=" O   PHE B 995 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ARG B 994 " --> pdb=" O   GLU B1005 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLU B1005 " --> pdb=" O   ARG B 994 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   GLY B 996 " --> pdb=" O   CYS B1003 " (cutoff:3.500A)
      removed outlier: 9.944A  pdb=" N   ARG B1001 " --> pdb=" O   HIS B1016 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   HIS B1016 " --> pdb=" O   ARG B1001 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   CYS B1003 " --> pdb=" O   THR B1014 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   LEU B1024 " --> pdb=" O   PHE B1068 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   LEU B1077 " --> pdb=" O   GLN B1089 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLN B1089 " --> pdb=" O   LEU B1077 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU B1079 " --> pdb=" O   ARG B1087 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1109 through 1110

    297 hydrogen bonds defined for protein.
    810 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: 4.64

  Time building geometry restraints manager: 2.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3173
        1.34 -     1.46: 2000
        1.46 -     1.57: 3911
        1.57 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 9105
  Sorted by residual:
  bond pdb=" C   TRP B 205 "
       pdb=" N   SER B 206 "
    ideal  model  delta    sigma   weight residual
    1.332  1.324  0.008 1.40e-02 5.10e+03 3.59e-01
  bond pdb=" C   GLY C1176 "
       pdb=" O   GLY C1176 "
    ideal  model  delta    sigma   weight residual
    1.239  1.235  0.004 7.10e-03 1.98e+04 3.23e-01
  bond pdb=" CB  VAL B 582 "
       pdb=" CG2 VAL B 582 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.019 3.30e-02 9.18e+02 3.17e-01
  bond pdb=" CA  HIS B1069 "
       pdb=" CB  HIS B1069 "
    ideal  model  delta    sigma   weight residual
    1.531  1.513  0.018 3.28e-02 9.30e+02 2.92e-01
  bond pdb=" CA  PHE B  74 "
       pdb=" C   PHE B  74 "
    ideal  model  delta    sigma   weight residual
    1.526  1.520  0.006 1.20e-02 6.94e+03 2.35e-01
  ... (remaining 9100 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 12141
        1.24 -     2.48: 134
        2.48 -     3.72: 59
        3.72 -     4.96: 3
        4.96 -     6.20: 1
  Bond angle restraints: 12338
  Sorted by residual:
  angle pdb=" CA  GLY C1176 "
        pdb=" C   GLY C1176 "
        pdb=" N   ALA C1177 "
      ideal   model   delta    sigma   weight residual
     118.95  116.70    2.25 1.06e+00 8.90e-01 4.52e+00
  angle pdb=" C   ARG B1096 "
        pdb=" N   ALA B1097 "
        pdb=" CA  ALA B1097 "
      ideal   model   delta    sigma   weight residual
     121.54  125.47   -3.93 1.91e+00 2.74e-01 4.23e+00
  angle pdb=" C   GLY B 406 "
        pdb=" N   ARG B 407 "
        pdb=" CA  ARG B 407 "
      ideal   model   delta    sigma   weight residual
     121.54  125.32   -3.78 1.91e+00 2.74e-01 3.93e+00
  angle pdb=" N   GLY C1176 "
        pdb=" CA  GLY C1176 "
        pdb=" C   GLY C1176 "
      ideal   model   delta    sigma   weight residual
     115.80  112.62    3.18 1.74e+00 3.30e-01 3.34e+00
  angle pdb=" CA  LEU B 957 "
        pdb=" CB  LEU B 957 "
        pdb=" CG  LEU B 957 "
      ideal   model   delta    sigma   weight residual
     116.30  122.50   -6.20 3.50e+00 8.16e-02 3.14e+00
  ... (remaining 12333 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 5154
       17.14 -    34.28: 190
       34.28 -    51.42: 26
       51.42 -    68.57: 3
       68.57 -    85.71: 2
  Dihedral angle restraints: 5375
    sinusoidal: 2198
      harmonic: 3177
  Sorted by residual:
  dihedral pdb=" N   GLU B 135 "
           pdb=" CA  GLU B 135 "
           pdb=" CB  GLU B 135 "
           pdb=" CG  GLU B 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.99  -58.01     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   VAL B1098 "
           pdb=" CA  VAL B1098 "
           pdb=" CB  VAL B1098 "
           pdb=" CG1 VAL B1098 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  128.41   51.59     3      1.50e+01 4.44e-03 9.03e+00
  dihedral pdb=" CA  GLU B1048 "
           pdb=" CB  GLU B1048 "
           pdb=" CG  GLU B1048 "
           pdb=" CD  GLU B1048 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  111.37  -51.37     3      1.50e+01 4.44e-03 9.01e+00
  ... (remaining 5372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 715
       0.026 -    0.051: 347
       0.051 -    0.077: 90
       0.077 -    0.103: 53
       0.103 -    0.129: 44
  Chirality restraints: 1249
  Sorted by residual:
  chirality pdb=" CA  ILE B 666 "
            pdb=" N   ILE B 666 "
            pdb=" C   ILE B 666 "
            pdb=" CB  ILE B 666 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  ILE B 561 "
            pdb=" N   ILE B 561 "
            pdb=" C   ILE B 561 "
            pdb=" CB  ILE B 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  chirality pdb=" CA  VAL B 214 "
            pdb=" N   VAL B 214 "
            pdb=" C   VAL B 214 "
            pdb=" CB  VAL B 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 1246 not shown)

  Planarity restraints: 1678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 521 "   -0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO B 522 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 522 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 522 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 797 "   -0.024 5.00e-02 4.00e+02   3.61e-02 2.09e+00
        pdb=" N   PRO B 798 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 798 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 798 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 183 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 184 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 184 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 184 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1675 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 706
        2.74 -     3.28: 7861
        3.28 -     3.82: 14579
        3.82 -     4.36: 18907
        4.36 -     4.90: 32783
  Nonbonded interactions: 74836
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 199 "
            pdb=" OD1 ASP B 472 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ALA B  67 "
            pdb=" NH2 ARG B 220 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   ARG B 154 "
            pdb=" OH  TYR B 177 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD2 ASP B  63 "
            pdb=" OH  TYR B 270 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER B 727 "
            pdb=" OG1 THR B 736 "
     model   vdw
     2.281 3.040
  ... (remaining 74831 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.910
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9105  Z= 0.198
  Angle     :  0.424   6.204  12338  Z= 0.223
  Chirality :  0.040   0.129   1249
  Planarity :  0.004   0.039   1678
  Dihedral  :  9.140  85.707   3377
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  2.75 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1121
  helix: -0.90 (0.98), residues: 33
  sheet:  0.75 (0.28), residues: 351
  loop :  0.41 (0.23), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B 129 
 PHE   0.007   0.001   PHE B 790 
 TYR   0.009   0.001   TYR B1130 
 ARG   0.003   0.000   ARG B1136 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A   37 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7885 (ttm-80)
REVERT: B  135 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7975 (mm-30)
REVERT: B  149 GLN cc_start: 0.8975 (mt0) cc_final: 0.8766 (mt0)
REVERT: B  204 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7376 (ttm110)
REVERT: B  298 MET cc_start: 0.9173 (mmp) cc_final: 0.8941 (mmp)
REVERT: B  360 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7317 (mm-30)
REVERT: B  402 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7304 (mtt-85)
REVERT: B  411 GLU cc_start: 0.8334 (tt0) cc_final: 0.8134 (tt0)
REVERT: B  420 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7620 (mtp85)
REVERT: B  421 LYS cc_start: 0.8292 (tttt) cc_final: 0.7804 (ttmp)
REVERT: B 1103 GLN cc_start: 0.7912 (pm20) cc_final: 0.7611 (pm20)
REVERT: B 1118 GLU cc_start: 0.8477 (tt0) cc_final: 0.7807 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 76
  average time/residue: 1.8882
  time to fit residues: 151.1135
Evaluate side-chains
  53 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue 1098 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 100 optimal weight:    6.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 191 GLN
B 260 GLN
B 271 GLN
B 405 GLN
B 803 GLN
B 816 GLN
B 956 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.088805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.066150 restraints weight = 12511.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 2.71
r_work: 0.2623 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2459 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   9105  Z= 0.415
  Angle     :  0.545   7.957  12338  Z= 0.289
  Chirality :  0.044   0.139   1249
  Planarity :  0.005   0.040   1678
  Dihedral  :  4.226  47.149   1321
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  4.81 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.25), residues: 1121
  helix: -0.24 (1.01), residues: 33
  sheet:  0.60 (0.28), residues: 333
  loop :  0.26 (0.23), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B 594 
 PHE   0.013   0.002   PHE B 120 
 TYR   0.010   0.001   TYR B 636 
 ARG   0.005   0.000   ARG B 440 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.957 
Fit side-chains
REVERT: B  135 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8077 (mm-30)
REVERT: B  149 GLN cc_start: 0.8990 (mt0) cc_final: 0.8762 (mt0)
REVERT: B  202 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7523 (mt-10)
REVERT: B  360 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7298 (mm-30)
REVERT: B  401 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5717 (mtt90)
REVERT: B  411 GLU cc_start: 0.8103 (tt0) cc_final: 0.7852 (tt0)
REVERT: B  420 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7702 (mtp85)
REVERT: B  421 LYS cc_start: 0.8169 (tttt) cc_final: 0.7772 (ttmp)
REVERT: B 1009 ARG cc_start: 0.7819 (mmt-90) cc_final: 0.7575 (mmt-90)
REVERT: B 1103 GLN cc_start: 0.8029 (pm20) cc_final: 0.7708 (pm20)
REVERT: B 1164 ASP cc_start: 0.8376 (m-30) cc_final: 0.8170 (m-30)
  outliers start: 17
  outliers final: 5
  residues processed: 70
  average time/residue: 1.7309
  time to fit residues: 128.2192
Evaluate side-chains
  61 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1098 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
B 271 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.089578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.066983 restraints weight = 12588.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 2.74
r_work: 0.2646 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9105  Z= 0.222
  Angle     :  0.473   6.907  12338  Z= 0.251
  Chirality :  0.041   0.132   1249
  Planarity :  0.004   0.042   1678
  Dihedral  :  4.070  48.654   1319
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  6.06 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1121
  helix:  0.09 (1.05), residues: 33
  sheet:  0.61 (0.27), residues: 339
  loop :  0.19 (0.23), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.001   HIS B 594 
 PHE   0.010   0.001   PHE B 790 
 TYR   0.008   0.001   TYR B1130 
 ARG   0.004   0.000   ARG B 440 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 1.016 
Fit side-chains
REVERT: B  149 GLN cc_start: 0.8928 (mt0) cc_final: 0.8694 (mt0)
REVERT: B  411 GLU cc_start: 0.8090 (tt0) cc_final: 0.7826 (tt0)
REVERT: B  420 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7643 (mtp85)
REVERT: B  421 LYS cc_start: 0.8011 (tttt) cc_final: 0.7602 (ttmp)
REVERT: B 1009 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7697 (mmt-90)
REVERT: B 1048 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6463 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7670 (pm20)
REVERT: B 1164 ASP cc_start: 0.8355 (m-30) cc_final: 0.8104 (m-30)
  outliers start: 17
  outliers final: 8
  residues processed: 65
  average time/residue: 1.5543
  time to fit residues: 107.7980
Evaluate side-chains
  64 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   chunk 108 optimal weight:    3.9990
   chunk 102 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 98 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.089205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.066563 restraints weight = 12613.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 2.75
r_work: 0.2641 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9105  Z= 0.256
  Angle     :  0.478   7.082  12338  Z= 0.252
  Chirality :  0.042   0.132   1249
  Planarity :  0.004   0.042   1678
  Dihedral  :  4.066  47.959   1319
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  6.64 %
    Favored  : 91.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.25), residues: 1121
  helix:  0.13 (1.04), residues: 33
  sheet:  0.62 (0.27), residues: 345
  loop :  0.21 (0.23), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B 956 
 PHE   0.011   0.001   PHE B 790 
 TYR   0.008   0.001   TYR B1130 
 ARG   0.005   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.015 
Fit side-chains
REVERT: B  149 GLN cc_start: 0.8927 (mt0) cc_final: 0.8694 (mt0)
REVERT: B  411 GLU cc_start: 0.8070 (tt0) cc_final: 0.7822 (tt0)
REVERT: B  420 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7696 (mtp85)
REVERT: B  421 LYS cc_start: 0.8023 (tttt) cc_final: 0.7593 (ttmp)
REVERT: B 1009 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7691 (mmt-90)
REVERT: B 1048 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6484 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7696 (pm20)
REVERT: B 1164 ASP cc_start: 0.8361 (m-30) cc_final: 0.8104 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 65
  average time/residue: 1.4894
  time to fit residues: 103.4271
Evaluate side-chains
  63 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 61 optimal weight:    0.3980
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.090221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.067792 restraints weight = 12554.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.74
r_work: 0.2664 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2504 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9105  Z= 0.169
  Angle     :  0.454   6.630  12338  Z= 0.240
  Chirality :  0.041   0.134   1249
  Planarity :  0.004   0.046   1678
  Dihedral  :  3.952  49.779   1319
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  6.86 %
    Favored  : 91.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.25), residues: 1121
  helix:  0.05 (1.05), residues: 34
  sheet:  0.66 (0.27), residues: 345
  loop :  0.20 (0.23), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B 956 
 PHE   0.010   0.001   PHE B 790 
 TYR   0.007   0.001   TYR B1130 
 ARG   0.010   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8369 (tp) cc_final: 0.8123 (tm)
REVERT: B  149 GLN cc_start: 0.8920 (mt0) cc_final: 0.8689 (mt0)
REVERT: B  183 CYS cc_start: 0.8615 (m) cc_final: 0.7956 (m)
REVERT: B  298 MET cc_start: 0.8896 (mmp) cc_final: 0.8598 (mmt)
REVERT: B  401 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5718 (mtt90)
REVERT: B  411 GLU cc_start: 0.8081 (tt0) cc_final: 0.7876 (tt0)
REVERT: B  420 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7651 (mtp85)
REVERT: B 1048 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6394 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7686 (pm20)
  outliers start: 16
  outliers final: 8
  residues processed: 66
  average time/residue: 1.5274
  time to fit residues: 107.6284
Evaluate side-chains
  65 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0470
   chunk 110 optimal weight:   30.0000
   chunk 97 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.7878

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.090731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.068200 restraints weight = 12445.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.74
r_work: 0.2670 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2509 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9105  Z= 0.168
  Angle     :  0.449   6.523  12338  Z= 0.237
  Chirality :  0.041   0.132   1249
  Planarity :  0.004   0.047   1678
  Dihedral  :  3.894  50.522   1319
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  7.32 %
    Favored  : 90.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1121
  helix:  0.10 (1.05), residues: 34
  sheet:  0.68 (0.26), residues: 355
  loop :  0.24 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B 956 
 PHE   0.011   0.001   PHE B 790 
 TYR   0.007   0.001   TYR B1130 
 ARG   0.010   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8449 (tp) cc_final: 0.8200 (tm)
REVERT: B  149 GLN cc_start: 0.8921 (mt0) cc_final: 0.8688 (mt0)
REVERT: B  183 CYS cc_start: 0.8603 (m) cc_final: 0.8012 (m)
REVERT: B  298 MET cc_start: 0.8899 (mmp) cc_final: 0.8617 (mmt)
REVERT: B  401 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6057 (mtt90)
REVERT: B  411 GLU cc_start: 0.8099 (tt0) cc_final: 0.7894 (tt0)
REVERT: B  420 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7701 (mtp85)
REVERT: B 1048 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6404 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7679 (pm20)
  outliers start: 17
  outliers final: 9
  residues processed: 69
  average time/residue: 1.4765
  time to fit residues: 109.2564
Evaluate side-chains
  67 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  763 VAL
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 69 optimal weight:    0.0040
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.090654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.068249 restraints weight = 12488.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.74
r_work: 0.2674 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9105  Z= 0.166
  Angle     :  0.450   6.445  12338  Z= 0.236
  Chirality :  0.041   0.132   1249
  Planarity :  0.004   0.051   1678
  Dihedral  :  3.888  50.687   1319
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  7.67 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1121
  helix:  0.12 (1.05), residues: 34
  sheet:  0.62 (0.26), residues: 365
  loop :  0.34 (0.24), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B 956 
 PHE   0.011   0.001   PHE B 790 
 TYR   0.007   0.001   TYR B1130 
 ARG   0.012   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8450 (tp) cc_final: 0.8202 (tm)
REVERT: B  149 GLN cc_start: 0.8924 (mt0) cc_final: 0.8687 (mt0)
REVERT: B  183 CYS cc_start: 0.8573 (m) cc_final: 0.8072 (m)
REVERT: B  401 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6078 (mtt90)
REVERT: B  411 GLU cc_start: 0.8089 (tt0) cc_final: 0.7780 (OUTLIER)
REVERT: B  420 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7690 (mtp85)
REVERT: B  963 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8658 (p0)
REVERT: B 1009 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7749 (mmt180)
REVERT: B 1048 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6375 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7697 (pm20)
  outliers start: 15
  outliers final: 8
  residues processed: 64
  average time/residue: 1.5477
  time to fit residues: 105.6658
Evaluate side-chains
  64 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  763 VAL
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0370
   chunk 83 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.4462

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.089473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.066776 restraints weight = 12697.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 2.76
r_work: 0.2641 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9105  Z= 0.262
  Angle     :  0.482   6.869  12338  Z= 0.252
  Chirality :  0.042   0.132   1249
  Planarity :  0.004   0.056   1678
  Dihedral  :  3.774  34.548   1318
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  8.12 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.25), residues: 1121
  helix:  0.09 (1.05), residues: 34
  sheet:  0.71 (0.27), residues: 343
  loop :  0.27 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B 956 
 PHE   0.011   0.001   PHE B 790 
 TYR   0.008   0.001   TYR B1130 
 ARG   0.012   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8407 (tp) cc_final: 0.8149 (tm)
REVERT: B  149 GLN cc_start: 0.8933 (mt0) cc_final: 0.8693 (mt0)
REVERT: B  183 CYS cc_start: 0.8566 (m) cc_final: 0.7972 (m)
REVERT: B  401 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6076 (mtt90)
REVERT: B  420 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7690 (mtp85)
REVERT: B  421 LYS cc_start: 0.8032 (tttt) cc_final: 0.7500 (ttmt)
REVERT: B 1048 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6399 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7732 (pm20)
  outliers start: 15
  outliers final: 7
  residues processed: 62
  average time/residue: 1.6727
  time to fit residues: 110.0591
Evaluate side-chains
  62 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  763 VAL
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 26 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 97 optimal weight:    0.4980
   chunk 98 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.2342

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.089465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.066935 restraints weight = 12612.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 2.74
r_work: 0.2648 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2488 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9105  Z= 0.230
  Angle     :  0.475   6.672  12338  Z= 0.249
  Chirality :  0.041   0.133   1249
  Planarity :  0.004   0.058   1678
  Dihedral  :  3.750  33.642   1318
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  7.89 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1121
  helix:  0.10 (1.05), residues: 34
  sheet:  0.65 (0.26), residues: 353
  loop :  0.33 (0.23), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B 956 
 PHE   0.010   0.001   PHE B 790 
 TYR   0.008   0.001   TYR B1130 
 ARG   0.014   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8466 (tp) cc_final: 0.8211 (tm)
REVERT: B  149 GLN cc_start: 0.8927 (mt0) cc_final: 0.8681 (mt0)
REVERT: B  183 CYS cc_start: 0.8585 (m) cc_final: 0.8079 (m)
REVERT: B  401 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6127 (mtt90)
REVERT: B  420 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7699 (mtp85)
REVERT: B  844 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8456 (mm)
REVERT: B 1048 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6414 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7694 (pm20)
  outliers start: 14
  outliers final: 9
  residues processed: 64
  average time/residue: 1.6138
  time to fit residues: 110.0992
Evaluate side-chains
  65 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  763 VAL
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1169 ILE
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    0.0270
   chunk 59 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 90 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
B 260 GLN
** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.090513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.067912 restraints weight = 12584.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 2.76
r_work: 0.2666 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2506 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9105  Z= 0.169
  Angle     :  0.461   6.390  12338  Z= 0.242
  Chirality :  0.041   0.137   1249
  Planarity :  0.004   0.061   1678
  Dihedral  :  3.650  32.221   1318
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.24 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.25), residues: 1121
  helix:  0.14 (1.05), residues: 34
  sheet:  0.65 (0.26), residues: 359
  loop :  0.36 (0.24), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B 956 
 PHE   0.011   0.001   PHE B 790 
 TYR   0.007   0.001   TYR B1130 
 ARG   0.015   0.000   ARG B 204 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8466 (tp) cc_final: 0.8220 (tm)
REVERT: B  149 GLN cc_start: 0.8922 (mt0) cc_final: 0.8709 (mt0)
REVERT: B  183 CYS cc_start: 0.8580 (m) cc_final: 0.8118 (m)
REVERT: B  204 ARG cc_start: 0.7564 (ttm110) cc_final: 0.6756 (ttp-110)
REVERT: B  401 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.5804 (mtt90)
REVERT: B  420 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7711 (mtp85)
REVERT: B  844 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8427 (mm)
REVERT: B 1048 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6389 (mt-10)
REVERT: B 1103 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7707 (pm20)
  outliers start: 13
  outliers final: 8
  residues processed: 64
  average time/residue: 1.5915
  time to fit residues: 108.4723
Evaluate side-chains
  66 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  401 ARG
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  763 VAL
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  844 LEU
Chi-restraints excluded: chain B residue  963 ASP
Chi-restraints excluded: chain B residue 1048 GLU
Chi-restraints excluded: chain B residue 1103 GLN
Chi-restraints excluded: chain C residue 1169 ILE
Chi-restraints excluded: chain C residue 1175 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0870
   chunk 55 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 86 optimal weight:    0.2980
   chunk 96 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.091348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.068817 restraints weight = 12543.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 2.75
r_work: 0.2685 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9105  Z= 0.142
  Angle     :  0.454   6.699  12338  Z= 0.238
  Chirality :  0.040   0.134   1249
  Planarity :  0.004   0.059   1678
  Dihedral  :  3.579  31.398   1318
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.01 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1121
  helix:  0.20 (1.06), residues: 34
  sheet:  0.67 (0.26), residues: 366
  loop :  0.39 (0.24), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.001   0.000   HIS B 956 
 PHE   0.010   0.001   PHE B 790 
 TYR   0.006   0.001   TYR B1130 
 ARG   0.014   0.000   ARG B 204 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6129.84 seconds
wall clock time: 108 minutes 45.18 seconds (6525.18 seconds total)