Starting phenix.real_space_refine
on Mon Jun 23 15:26:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avc_15678/06_2025/8avc_15678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avc_15678/06_2025/8avc_15678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avc_15678/06_2025/8avc_15678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avc_15678/06_2025/8avc_15678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avc_15678/06_2025/8avc_15678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avc_15678/06_2025/8avc_15678.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 11844 atoms to isotropic.
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
     Ni      3      6.56       5
     S      81      5.16       5
     C   11199      2.51       5
     N    2940      2.21       5
     O    3282      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17505
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4757
          Classifications: {'peptide': 593}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555}
    Chain: "C"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 4757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4757
          Classifications: {'peptide': 593}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555}
    Chain: "E"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 4757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4757
          Classifications: {'peptide': 593}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.69, per 1000 atoms: 0.55
  Number of scatterers: 17505
  At special positions: 0
  Unit cell: (137.614, 142.588, 169.116, 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)
     Ni      3     28.00
     S      81     16.00
     O    3282      8.00
     N    2940      7.00
     C   11199      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 411 " - pdb=" SG  CYS B 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 602 " - pdb=" SG  CYS B 672 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 350 " - pdb=" SG  CYS D 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 411 " - pdb=" SG  CYS D 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 434 " - pdb=" SG  CYS D 445 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 471 " - pdb=" SG  CYS D 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 486 " - pdb=" SG  CYS D 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 602 " - pdb=" SG  CYS D 672 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 117 " - pdb=" SG  CYS E 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 434 " - pdb=" SG  CYS F 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 471 " - pdb=" SG  CYS F 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 486 " - pdb=" SG  CYS F 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 602 " - pdb=" SG  CYS F 672 " 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=0, symmetry=0
  Time building additional restraints: 4.34
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  4362 Ramachandran restraints generated.
    2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4212

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 42 sheets defined
      16.6% alpha, 35.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 45
      removed outlier: 3.823A  pdb=" N   ILE A  45 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.655A  pdb=" N   GLN A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.847A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 116
    Processing helix  chain 'A' and resid 130 through 138
      removed outlier: 3.758A  pdb=" N   VAL A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 160
    Processing helix  chain 'B' and resid 375 through 377
      No H-bonds generated for 'chain 'B' and resid 375 through 377'
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.975A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 736
    Processing helix  chain 'C' and resid 23 through 45
      removed outlier: 3.594A  pdb=" N   ILE C  45 " --> pdb=" O   ARG C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 50
      removed outlier: 3.629A  pdb=" N   GLN C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 50'
    Processing helix  chain 'C' and resid 71 through 89
      removed outlier: 3.884A  pdb=" N   SER C  88 " --> pdb=" O   GLN C  84 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU C  89 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 116
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.631A  pdb=" N   VAL C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 160
    Processing helix  chain 'D' and resid 528 through 533
      removed outlier: 3.819A  pdb=" N   VAL D 533 " --> pdb=" O   ASP D 530 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 666 through 671
    Processing helix  chain 'D' and resid 732 through 736
    Processing helix  chain 'E' and resid 23 through 45
      removed outlier: 3.527A  pdb=" N   ILE E  45 " --> pdb=" O   ARG E  41 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 50
      removed outlier: 3.940A  pdb=" N   SER E  50 " --> pdb=" O   SER E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 89
      removed outlier: 3.793A  pdb=" N   SER E  88 " --> pdb=" O   GLN E  84 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU E  89 " --> pdb=" O   VAL E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 91 through 116
    Processing helix  chain 'E' and resid 130 through 138
      removed outlier: 3.801A  pdb=" N   VAL E 134 " --> pdb=" O   SER E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 160
    Processing helix  chain 'F' and resid 360 through 362
      No H-bonds generated for 'chain 'F' and resid 360 through 362'
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing helix  chain 'F' and resid 528 through 533
      removed outlier: 3.868A  pdb=" N   VAL F 532 " --> pdb=" O   LEU F 528 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 732 through 736
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246
      removed outlier: 3.679A  pdb=" N   LEU B 240 " --> pdb=" O   ASP B 257 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LEU B 242 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   SER B 255 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   MET B 244 " --> pdb=" O   LYS B 253 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LYS B 253 " --> pdb=" O   MET B 244 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286
    Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341
      removed outlier: 3.571A  pdb=" N   GLU B 372 " --> pdb=" O   ARG B 368 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341
      removed outlier: 6.833A  pdb=" N   CYS B 410 " --> pdb=" O   HIS B 417 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   HIS B 417 " --> pdb=" O   CYS B 410 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   CYS B 416 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 433 through 436
    Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.250A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.250A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545
      removed outlier: 3.672A  pdb=" N   VAL B 541 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   SER B 555 " --> pdb=" O   VAL B 541 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   ALA B 543 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LYS B 553 " --> pdb=" O   ALA B 543 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648
    Processing sheet with id=AB4, first strand: chain 'B' and resid 690 through 694
      removed outlier: 5.842A  pdb=" N   TYR B 677 " --> pdb=" O   VAL B 693 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 748
      removed outlier: 5.459A  pdb=" N   LEU B 742 " --> pdb=" O   THR B 757 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   THR B 757 " --> pdb=" O   LEU B 742 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   ALA B 744 " --> pdb=" O   SER B 755 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   SER B 755 " --> pdb=" O   ALA B 744 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE B 753 " --> pdb=" O   PRO B 746 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787
      removed outlier: 3.599A  pdb=" N   TYR B 767 " --> pdb=" O   VAL B 812 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 240 through 246
      removed outlier: 5.457A  pdb=" N   GLY D 241 " --> pdb=" O   ASP D 257 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP D 257 " --> pdb=" O   GLY D 241 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 286
    Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334
    Processing sheet with id=AC1, first strand: chain 'D' and resid 337 through 340
      removed outlier: 3.805A  pdb=" N   GLU D 372 " --> pdb=" O   ARG D 368 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 417
      removed outlier: 7.468A  pdb=" N   CYS D 416 " --> pdb=" O   THR E  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'D' and resid 433 through 436
    Processing sheet with id=AC4, first strand: chain 'D' and resid 482 through 484
      removed outlier: 4.177A  pdb=" N   LEU D 462 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 482 through 484
      removed outlier: 4.177A  pdb=" N   LEU D 462 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 539 through 545
      removed outlier: 4.102A  pdb=" N   VAL D 541 " --> pdb=" O   SER D 555 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER D 555 " --> pdb=" O   VAL D 541 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ALA D 543 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LYS D 553 " --> pdb=" O   ALA D 543 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 582 through 586
    Processing sheet with id=AC8, first strand: chain 'D' and resid 643 through 648
    Processing sheet with id=AC9, first strand: chain 'D' and resid 687 through 694
      removed outlier: 5.788A  pdb=" N   TYR D 677 " --> pdb=" O   VAL D 693 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 739 through 745
    Processing sheet with id=AD2, first strand: chain 'D' and resid 782 through 787
      removed outlier: 3.642A  pdb=" N   TYR D 767 " --> pdb=" O   VAL D 812 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS D 773 " --> pdb=" O   GLN D 806 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 240 through 246
      removed outlier: 6.045A  pdb=" N   GLY F 241 " --> pdb=" O   ASP F 257 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ASP F 257 " --> pdb=" O   GLY F 241 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'F' and resid 279 through 286
    Processing sheet with id=AD5, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AD6, first strand: chain 'F' and resid 337 through 341
    Processing sheet with id=AD7, first strand: chain 'F' and resid 433 through 436
    Processing sheet with id=AD8, first strand: chain 'F' and resid 482 through 484
      removed outlier: 4.479A  pdb=" N   LEU F 462 " --> pdb=" O   LYS F 484 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'F' and resid 482 through 484
      removed outlier: 4.479A  pdb=" N   LEU F 462 " --> pdb=" O   LYS F 484 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'F' and resid 539 through 545
      removed outlier: 5.594A  pdb=" N   ASN F 540 " --> pdb=" O   GLU F 557 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLU F 557 " --> pdb=" O   ASN F 540 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'F' and resid 582 through 586
    Processing sheet with id=AE3, first strand: chain 'F' and resid 643 through 648
    Processing sheet with id=AE4, first strand: chain 'F' and resid 687 through 694
      removed outlier: 5.818A  pdb=" N   TYR F 677 " --> pdb=" O   VAL F 693 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'F' and resid 739 through 745
    Processing sheet with id=AE6, first strand: chain 'F' and resid 782 through 787
      removed outlier: 3.544A  pdb=" N   TYR F 767 " --> pdb=" O   VAL F 812 " (cutoff:3.500A)

    790 hydrogen bonds defined for protein.
    2076 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: 6.85

  Time building geometry restraints manager: 5.06 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2938
        1.32 -     1.46: 6297
        1.46 -     1.59: 8585
        1.59 -     1.73: 0
        1.73 -     1.87: 114
  Bond restraints: 17934
  Sorted by residual:
  bond pdb=" CB  GLN C  96 "
       pdb=" CG  GLN C  96 "
    ideal  model  delta    sigma   weight residual
    1.520  1.424  0.096 3.00e-02 1.11e+03 1.02e+01
  bond pdb=" CD  GLN C  96 "
       pdb=" NE2 GLN C  96 "
    ideal  model  delta    sigma   weight residual
    1.328  1.274  0.054 2.10e-02 2.27e+03 6.67e+00
  bond pdb=" CB  ASN C  99 "
       pdb=" CG  ASN C  99 "
    ideal  model  delta    sigma   weight residual
    1.516  1.455  0.061 2.50e-02 1.60e+03 5.93e+00
  bond pdb=" CG  ASN A 103 "
       pdb=" OD1 ASN A 103 "
    ideal  model  delta    sigma   weight residual
    1.231  1.186  0.045 1.90e-02 2.77e+03 5.51e+00
  bond pdb=" CG  GLN C  96 "
       pdb=" CD  GLN C  96 "
    ideal  model  delta    sigma   weight residual
    1.516  1.574 -0.058 2.50e-02 1.60e+03 5.44e+00
  ... (remaining 17929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.53: 24265
        3.53 -     7.06: 147
        7.06 -    10.59: 25
       10.59 -    14.12: 2
       14.12 -    17.65: 2
  Bond angle restraints: 24441
  Sorted by residual:
  angle pdb=" CB  GLN C  96 "
        pdb=" CG  GLN C  96 "
        pdb=" CD  GLN C  96 "
      ideal   model   delta    sigma   weight residual
     112.60   94.95   17.65 1.70e+00 3.46e-01 1.08e+02
  angle pdb=" N   CYS D 434 "
        pdb=" CA  CYS D 434 "
        pdb=" C   CYS D 434 "
      ideal   model   delta    sigma   weight residual
     108.38  116.42   -8.04 1.35e+00 5.49e-01 3.55e+01
  angle pdb=" N   GLN C  96 "
        pdb=" CA  GLN C  96 "
        pdb=" C   GLN C  96 "
      ideal   model   delta    sigma   weight residual
     111.36  104.87    6.49 1.09e+00 8.42e-01 3.55e+01
  angle pdb=" C   ASN A 103 "
        pdb=" CA  ASN A 103 "
        pdb=" CB  ASN A 103 "
      ideal   model   delta    sigma   weight residual
     110.63  120.80  -10.17 1.85e+00 2.92e-01 3.02e+01
  angle pdb=" CA  ASN A 103 "
        pdb=" CB  ASN A 103 "
        pdb=" CG  ASN A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  118.09   -5.49 1.00e+00 1.00e+00 3.02e+01
  ... (remaining 24436 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 10063
       17.59 -    35.19: 653
       35.19 -    52.78: 101
       52.78 -    70.38: 27
       70.38 -    87.97: 10
  Dihedral angle restraints: 10854
    sinusoidal: 4368
      harmonic: 6486
  Sorted by residual:
  dihedral pdb=" CA  ILE D 501 "
           pdb=" C   ILE D 501 "
           pdb=" N   PHE D 502 "
           pdb=" CA  PHE D 502 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.16   42.84     0      5.00e+00 4.00e-02 7.34e+01
  dihedral pdb=" CB  CYS B 350 "
           pdb=" SG  CYS B 350 "
           pdb=" SG  CYS B 410 "
           pdb=" CB  CYS B 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -22.47  -63.53     1      1.00e+01 1.00e-02 5.32e+01
  dihedral pdb=" CB  CYS B 486 "
           pdb=" SG  CYS B 486 "
           pdb=" SG  CYS B 496 "
           pdb=" CB  CYS B 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   30.11   62.89     1      1.00e+01 1.00e-02 5.23e+01
  ... (remaining 10851 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 2636
       0.106 -    0.211: 154
       0.211 -    0.317: 8
       0.317 -    0.422: 0
       0.422 -    0.528: 1
  Chirality restraints: 2799
  Sorted by residual:
  chirality pdb=" CA  ASN A 103 "
            pdb=" N   ASN A 103 "
            pdb=" C   ASN A 103 "
            pdb=" CB  ASN A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.97e+00
  chirality pdb=" CB  ILE E  69 "
            pdb=" CA  ILE E  69 "
            pdb=" CG1 ILE E  69 "
            pdb=" CG2 ILE E  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CG  LEU A  60 "
            pdb=" CB  LEU A  60 "
            pdb=" CD1 LEU A  60 "
            pdb=" CD2 LEU A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.21e+00
  ... (remaining 2796 not shown)

  Planarity restraints: 3078
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN C  96 "    0.022 2.00e-02 2.50e+03   4.64e-02 2.16e+01
        pdb=" CD  GLN C  96 "   -0.080 2.00e-02 2.50e+03
        pdb=" OE1 GLN C  96 "    0.029 2.00e-02 2.50e+03
        pdb=" NE2 GLN C  96 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 103 "    0.019 2.00e-02 2.50e+03   3.85e-02 1.48e+01
        pdb=" CG  ASN A 103 "   -0.067 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 103 "    0.026 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 103 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 759 "   -0.061 5.00e-02 4.00e+02   8.94e-02 1.28e+01
        pdb=" N   PRO B 760 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO B 760 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 760 "   -0.050 5.00e-02 4.00e+02
  ... (remaining 3075 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 191
        2.52 -     3.12: 13291
        3.12 -     3.71: 28949
        3.71 -     4.31: 39823
        4.31 -     4.90: 63889
  Nonbonded interactions: 146143
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C  96 "
            pdb=" O   ILE D 501 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" ND2 ASN A 103 "
            pdb=" N   LEU B 504 "
     model   vdw
     1.987 3.200
  nonbonded pdb=" NH1 ARG B 467 "
            pdb="NI    NI B 901 "
     model   vdw
     2.014 2.260
  nonbonded pdb=" NE2 GLN C  83 "
            pdb=" O   ALA C  98 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" OH  TYR B 409 "
            pdb=" CB  SER C 141 "
     model   vdw
     2.122 3.440
  ... (remaining 146138 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  Number of NCS constrained groups: 2
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.180
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     41.190
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
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      :  0.004   0.096  17955  Z= 0.169
  Angle     :  0.802  17.651  24483  Z= 0.445
  Chirality :  0.052   0.528   2799
  Planarity :  0.005   0.089   3078
  Dihedral  : 12.050  87.969   6579
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.31 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.17 (0.18), residues: 2181
  helix: -0.69 (0.26), residues: 327
  sheet:  0.27 (0.17), residues: 847
  loop : -0.08 (0.21), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 447 
 HIS   0.006   0.001   HIS B 465 
 PHE   0.052   0.001   PHE D 502 
 TYR   0.019   0.001   TYR D 268 
 ARG   0.010   0.001   ARG C 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11941 (  743)
  hydrogen bonds       : angle       6.70910 ( 2076)
  SS BOND              : bond        0.00494 (   21)
  SS BOND              : angle       1.90445 (   42)
  covalent geometry    : bond        0.00360 (17934)
  covalent geometry    : angle       0.79906 (24441)

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

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

  4362 Ramachandran restraints generated.
    2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4362 Ramachandran restraints generated.
    2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9694 (mt) cc_final: 0.9448 (mt)
REVERT: A  102 GLU cc_start: 0.8539 (mp0) cc_final: 0.8269 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1165
  time to fit residues: 5.2697
Evaluate side-chains
  32 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.136 
Evaluate side-chains
  35 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5244 (ppp) cc_final: 0.4220 (pmm)
REVERT: B  443 MET cc_start: 0.9131 (tpp) cc_final: 0.8734 (tpp)
REVERT: B  548 ASN cc_start: 0.8571 (m-40) cc_final: 0.8305 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1931
  time to fit residues: 9.4849
Evaluate side-chains
  31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 184 optimal weight:    6.9990
   chunk 165 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 56 optimal weight:    0.4980
   chunk 111 optimal weight:    0.7980
   chunk 88 optimal weight:    0.4980
   chunk 171 optimal weight:    0.3980
   chunk 66 optimal weight:    7.9990
   chunk 104 optimal weight:    0.0670
   chunk 127 optimal weight:    0.0570
   chunk 198 optimal weight:    9.9990
   overall best weight:    0.3036
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 363 GLN
B 489 GLN
B 567 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.049462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.037636 restraints weight = 6452.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.039205 restraints weight = 4587.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.040495 restraints weight = 3485.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.2856
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.077416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.061512 restraints weight = 30285.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.061264 restraints weight = 20967.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.061363 restraints weight = 10372.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          1.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17955  Z= 0.154
  Angle     :  0.686   8.103  24483  Z= 0.368
  Chirality :  0.048   0.181   2799
  Planarity :  0.005   0.052   3078
  Dihedral  :  5.481  57.666   2367
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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:  0.21 (0.18), residues: 2181
  helix:  0.14 (0.27), residues: 300
  sheet:  0.29 (0.16), residues: 909
  loop :  0.18 (0.22), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 447 
 HIS   0.004   0.001   HIS F 418 
 PHE   0.008   0.001   PHE D 348 
 TYR   0.029   0.002   TYR D 333 
 ARG   0.007   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05028 (  743)
  hydrogen bonds       : angle       6.15232 ( 2076)
  SS BOND              : bond        0.00411 (   21)
  SS BOND              : angle       1.43663 (   42)
  covalent geometry    : bond        0.00323 (17934)
  covalent geometry    : angle       0.68394 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.9272 (mt) cc_final: 0.8752 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1372
  time to fit residues: 5.8881
Evaluate side-chains
  32 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.114 
Evaluate side-chains
  43 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5101 (ppp) cc_final: 0.4405 (pmm)
REVERT: B  503 LEU cc_start: 0.9314 (tt) cc_final: 0.9059 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1459
  time to fit residues: 8.7028
Evaluate side-chains
  33 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 197 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 130 optimal weight:    5.9990
   chunk 91 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 162 optimal weight:    0.0980
   chunk 178 optimal weight:    6.9990
   chunk 142 optimal weight:    0.0870
   chunk 123 optimal weight:    0.7980
   chunk 192 optimal weight:    0.4980
   overall best weight:    0.4358
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.051382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.037404 restraints weight = 6214.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.038921 restraints weight = 4672.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.040198 restraints weight = 3686.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.077090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.061106 restraints weight = 31248.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.062332 restraints weight = 25408.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.062607 restraints weight = 10377.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
moved from start:          1.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.173  17955  Z= 0.270
  Angle     :  0.895  14.244  24483  Z= 0.484
  Chirality :  0.054   0.381   2799
  Planarity :  0.008   0.055   3078
  Dihedral  :  5.524  32.999   2367
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  5.19 %
    Favored  : 93.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.09 (0.18), residues: 2181
  helix: -0.08 (0.29), residues: 303
  sheet:  0.28 (0.16), residues: 906
  loop : -0.25 (0.20), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.004   TRP B 581 
 HIS   0.022   0.003   HIS D 478 
 PHE   0.099   0.005   PHE D 403 
 TYR   0.093   0.008   TYR B 420 
 ARG   0.023   0.002   ARG E  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  743)
  hydrogen bonds       : angle       6.32524 ( 2076)
  SS BOND              : bond        0.00679 (   21)
  SS BOND              : angle       1.47115 (   42)
  covalent geometry    : bond        0.00632 (17934)
  covalent geometry    : angle       0.89319 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.3459 (p) cc_final: 0.3062 (p)
REVERT: A  101 LEU cc_start: 0.9252 (mt) cc_final: 0.8991 (mt)
REVERT: A  102 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8396 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 39
  average time/residue: 0.1314
  time to fit residues: 5.6853
Evaluate side-chains
  27 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.116 
Evaluate side-chains
  47 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5181 (ppp) cc_final: 0.4240 (pmm)
  outliers start: 5
  outliers final: 2
  residues processed: 46
  average time/residue: 0.1449
  time to fit residues: 9.2982
Evaluate side-chains
  34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 90 optimal weight:    0.0870
   chunk 55 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0370
   chunk 74 optimal weight:    0.9990
   chunk 137 optimal weight:    3.9990
   chunk 40 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 13 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 153 optimal weight:    6.9990
   overall best weight:    1.0240
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  83 GLN

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.052176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.037803 restraints weight = 6297.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.039337 restraints weight = 4678.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.040665 restraints weight = 3694.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.078146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.062454 restraints weight = 31982.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.063737 restraints weight = 25248.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.063982 restraints weight = 10513.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          1.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.173  17955  Z= 0.308
  Angle     :  0.894  14.244  24483  Z= 0.484
  Chirality :  0.054   0.381   2799
  Planarity :  0.008   0.081   3078
  Dihedral  :  5.524  32.999   2367
  Min Nonbonded Distance : 1.175

Molprobity Statistics.
  All-atom Clashscore : 28.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.09 (0.18), residues: 2181
  helix: -0.08 (0.29), residues: 303
  sheet:  0.28 (0.16), residues: 906
  loop : -0.25 (0.20), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.004   TRP B 581 
 HIS   0.022   0.003   HIS D 478 
 PHE   0.099   0.005   PHE D 403 
 TYR   0.093   0.008   TYR D 420 
 ARG   0.023   0.002   ARG E  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  743)
  hydrogen bonds       : angle       6.32524 ( 2076)
  SS BOND              : bond        0.00679 (   21)
  SS BOND              : angle       1.47115 (   42)
  covalent geometry    : bond        0.00665 (17934)
  covalent geometry    : angle       0.89219 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.9621 (tppt) cc_final: 0.9413 (tttt)
REVERT: A  101 LEU cc_start: 0.9228 (mt) cc_final: 0.8951 (mt)
REVERT: A  102 GLU cc_start: 0.9093 (tp30) cc_final: 0.8853 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1168
  time to fit residues: 5.4829
Evaluate side-chains
  28 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.116 
Evaluate side-chains
  41 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5182 (ppp) cc_final: 0.4247 (pmm)
REVERT: B  273 LEU cc_start: 0.9564 (pp) cc_final: 0.9288 (tt)
REVERT: B  443 MET cc_start: 0.9194 (tpt) cc_final: 0.8925 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1411
  time to fit residues: 8.2638
Evaluate side-chains
  34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 36 optimal weight:    0.0010
   chunk 216 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0970
   chunk 214 optimal weight:    0.0040
   chunk 213 optimal weight:    0.9990
   chunk 190 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 114 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0040
   chunk 149 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.1408
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.052750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.039149 restraints weight = 6161.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.040795 restraints weight = 4543.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.042123 restraints weight = 3559.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.078292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.062681 restraints weight = 31281.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.063861 restraints weight = 24947.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.064174 restraints weight = 10398.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
moved from start:          1.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.152  17955  Z= 0.286
  Angle     :  0.972  15.729  24483  Z= 0.513
  Chirality :  0.057   0.423   2799
  Planarity :  0.008   0.059   3078
  Dihedral  :  5.619  30.195   2367
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.27 (0.18), residues: 2181
  helix: -0.72 (0.27), residues: 303
  sheet:  0.25 (0.16), residues: 906
  loop : -0.26 (0.20), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.005   TRP B 581 
 HIS   0.021   0.004   HIS D 478 
 PHE   0.074   0.004   PHE B 403 
 TYR   0.057   0.006   TYR D 464 
 ARG   0.022   0.002   ARG B 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05596 (  743)
  hydrogen bonds       : angle       6.62538 ( 2076)
  SS BOND              : bond        0.00366 (   21)
  SS BOND              : angle       1.25605 (   42)
  covalent geometry    : bond        0.00696 (17934)
  covalent geometry    : angle       0.97175 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9065 (tp30) cc_final: 0.8761 (mm-30)
REVERT: A  150 LEU cc_start: 0.9822 (tp) cc_final: 0.9529 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1257
  time to fit residues: 5.5094
Evaluate side-chains
  28 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.139 
Evaluate side-chains
  42 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5178 (ppp) cc_final: 0.4241 (pmm)
REVERT: B  273 LEU cc_start: 0.9606 (pp) cc_final: 0.9362 (tt)
REVERT: B  443 MET cc_start: 0.9340 (tpt) cc_final: 0.8981 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1506
  time to fit residues: 9.0036
Evaluate side-chains
  33 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 194 optimal weight:    0.0670
   chunk 184 optimal weight:   10.0000
   chunk 182 optimal weight:    0.4980
   chunk 18 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 213 optimal weight:    0.0470
   chunk 62 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    0.3416
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.050765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.038330 restraints weight = 6723.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.040038 restraints weight = 4670.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.041395 restraints weight = 3503.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.078197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.062406 restraints weight = 30944.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.063724 restraints weight = 24806.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.063900 restraints weight = 10175.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          1.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.435  17955  Z= 0.454
  Angle     :  0.997  16.480  24483  Z= 0.524
  Chirality :  0.057   0.423   2799
  Planarity :  0.008   0.059   3078
  Dihedral  :  5.619  30.195   2367
  Min Nonbonded Distance : 1.280

Molprobity Statistics.
  All-atom Clashscore : 26.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.27 (0.18), residues: 2181
  helix: -0.72 (0.27), residues: 303
  sheet:  0.25 (0.16), residues: 906
  loop : -0.26 (0.20), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.005   TRP B 581 
 HIS   0.021   0.004   HIS D 478 
 PHE   0.074   0.004   PHE D 403 
 TYR   0.057   0.006   TYR F 464 
 ARG   0.022   0.002   ARG B 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05596 (  743)
  hydrogen bonds       : angle       6.62538 ( 2076)
  SS BOND              : bond        0.16444 (   21)
  SS BOND              : angle       5.12567 (   42)
  covalent geometry    : bond        0.00757 (17934)
  covalent geometry    : angle       0.97479 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9032 (tp30) cc_final: 0.8720 (mm-30)
REVERT: A  150 LEU cc_start: 0.9804 (tp) cc_final: 0.9536 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1052
  time to fit residues: 4.2260
Evaluate side-chains
  28 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.115 
Evaluate side-chains
  41 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5174 (ppp) cc_final: 0.4235 (pmm)
REVERT: B  273 LEU cc_start: 0.9602 (pp) cc_final: 0.9355 (tt)
REVERT: B  443 MET cc_start: 0.9300 (tpt) cc_final: 0.8914 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1489
  time to fit residues: 8.5332
Evaluate side-chains
  34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 167 optimal weight:    9.9990
   chunk 206 optimal weight:    7.9990
   chunk 184 optimal weight:    7.9990
   chunk 213 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 191 optimal weight:    8.9990
   chunk 8 optimal weight:    0.4980
   chunk 186 optimal weight:    0.0770
   chunk 12 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   overall best weight:    3.1144
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.050765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.038440 restraints weight = 6591.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.040118 restraints weight = 4590.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.041479 restraints weight = 3456.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.078197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.062365 restraints weight = 31322.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.063646 restraints weight = 24958.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.063861 restraints weight = 10319.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          1.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.435  17955  Z= 0.454
  Angle     :  0.997  16.480  24483  Z= 0.524
  Chirality :  0.057   0.423   2799
  Planarity :  0.008   0.059   3078
  Dihedral  :  5.619  30.195   2367
  Min Nonbonded Distance : 1.280

Molprobity Statistics.
  All-atom Clashscore : 26.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.27 (0.18), residues: 2181
  helix: -0.72 (0.27), residues: 303
  sheet:  0.25 (0.16), residues: 906
  loop : -0.26 (0.20), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.005   TRP B 581 
 HIS   0.021   0.004   HIS D 478 
 PHE   0.074   0.004   PHE D 403 
 TYR   0.057   0.006   TYR B 464 
 ARG   0.022   0.002   ARG F 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05596 (  743)
  hydrogen bonds       : angle       6.62538 ( 2076)
  SS BOND              : bond        0.16444 (   21)
  SS BOND              : angle       5.12567 (   42)
  covalent geometry    : bond        0.00757 (17934)
  covalent geometry    : angle       0.97479 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9033 (tp30) cc_final: 0.8720 (mm-30)
REVERT: A  150 LEU cc_start: 0.9803 (tp) cc_final: 0.9536 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1001
  time to fit residues: 4.0375
Evaluate side-chains
  28 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.116 
Evaluate side-chains
  41 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5191 (ppp) cc_final: 0.4257 (pmm)
REVERT: B  273 LEU cc_start: 0.9608 (pp) cc_final: 0.9365 (tt)
REVERT: B  443 MET cc_start: 0.9313 (tpt) cc_final: 0.8926 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1457
  time to fit residues: 8.5720
Evaluate side-chains
  34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 173 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 195 optimal weight:    0.0570
   chunk 198 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 125 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 95 optimal weight:    0.3980
   chunk 24 optimal weight:    5.9990
   chunk 217 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.9900
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.050673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.038411 restraints weight = 6924.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.039972 restraints weight = 5061.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.041267 restraints weight = 3894.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.077920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.062240 restraints weight = 31115.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.063535 restraints weight = 25014.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.063789 restraints weight = 10582.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
moved from start:          1.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  17955  Z= 0.232
  Angle     :  0.923  12.666  24483  Z= 0.486
  Chirality :  0.058   0.413   2799
  Planarity :  0.009   0.105   3078
  Dihedral  :  5.636  25.972   2367
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 20.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.38 (0.18), residues: 2181
  helix: -0.82 (0.28), residues: 318
  sheet:  0.19 (0.16), residues: 906
  loop : -0.32 (0.21), residues: 957

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.005   TRP F 447 
 HIS   0.021   0.004   HIS F 478 
 PHE   0.034   0.003   PHE F 403 
 TYR   0.057   0.007   TYR F 464 
 ARG   0.022   0.002   ARG B 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05526 (  743)
  hydrogen bonds       : angle       6.55507 ( 2076)
  SS BOND              : bond        0.00493 (   21)
  SS BOND              : angle       1.20963 (   42)
  covalent geometry    : bond        0.00545 (17934)
  covalent geometry    : angle       0.92237 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.9018 (tp30) cc_final: 0.8778 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1363
  time to fit residues: 5.6536
Evaluate side-chains
  26 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.119 
Evaluate side-chains
  41 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5163 (ppp) cc_final: 0.4214 (pmm)
REVERT: B  273 LEU cc_start: 0.9560 (pp) cc_final: 0.9282 (tt)
REVERT: B  443 MET cc_start: 0.9389 (tpt) cc_final: 0.9009 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1527
  time to fit residues: 8.9541
Evaluate side-chains
  34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 135 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 121 optimal weight:    3.9990
   chunk 191 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 196 optimal weight:    0.6980
   chunk 102 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0670
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.7120
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.050842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.038589 restraints weight = 6868.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.040231 restraints weight = 4914.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.041561 restraints weight = 3723.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.077623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.062005 restraints weight = 31371.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.063327 restraints weight = 26515.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.063522 restraints weight = 11468.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
moved from start:          1.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  17955  Z= 0.214
  Angle     :  0.980  31.484  24483  Z= 0.492
  Chirality :  0.058   0.423   2799
  Planarity :  0.008   0.052   3078
  Dihedral  :  5.689  25.068   2367
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.50 (0.18), residues: 2181
  helix: -0.81 (0.28), residues: 318
  sheet:  0.18 (0.16), residues: 900
  loop : -0.53 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.005   TRP D 447 
 HIS   0.021   0.004   HIS F 478 
 PHE   0.016   0.003   PHE C  62 
 TYR   0.058   0.006   TYR A 140 
 ARG   0.031   0.002   ARG C  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 (  743)
  hydrogen bonds       : angle       6.47233 ( 2076)
  SS BOND              : bond        0.00487 (   21)
  SS BOND              : angle       1.11729 (   42)
  covalent geometry    : bond        0.00494 (17934)
  covalent geometry    : angle       0.97965 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.8978 (tp30) cc_final: 0.8734 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1164
  time to fit residues: 4.8741
Evaluate side-chains
  29 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.134 
Evaluate side-chains
  41 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5152 (ppp) cc_final: 0.4185 (pmm)
REVERT: B  273 LEU cc_start: 0.9584 (pp) cc_final: 0.9332 (tt)
REVERT: B  443 MET cc_start: 0.9423 (tpt) cc_final: 0.9080 (tpp)
REVERT: B  447 TRP cc_start: 0.8905 (p-90) cc_final: 0.8646 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1541
  time to fit residues: 8.9461
Evaluate side-chains
  31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 174 optimal weight:    0.4980
   chunk 93 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 177 optimal weight:    0.0980
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:    0.4980
   chunk 186 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 193 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.4780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.051212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.037993 restraints weight = 6966.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.039744 restraints weight = 4916.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.041141 restraints weight = 3742.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.077647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.061628 restraints weight = 31278.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.063191 restraints weight = 26160.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.063304 restraints weight = 11241.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          1.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  17955  Z= 0.214
  Angle     :  0.980  31.480  24483  Z= 0.492
  Chirality :  0.058   0.422   2799
  Planarity :  0.008   0.052   3078
  Dihedral  :  5.689  25.068   2367
  Min Nonbonded Distance : 1.728

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.50 (0.18), residues: 2181
  helix: -0.81 (0.28), residues: 318
  sheet:  0.18 (0.16), residues: 900
  loop : -0.53 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.005   TRP D 447 
 HIS   0.021   0.004   HIS F 478 
 PHE   0.016   0.003   PHE C  62 
 TYR   0.058   0.006   TYR A 140 
 ARG   0.031   0.002   ARG E  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 (  743)
  hydrogen bonds       : angle       6.47234 ( 2076)
  SS BOND              : bond        0.00487 (   21)
  SS BOND              : angle       1.11723 (   42)
  covalent geometry    : bond        0.00494 (17934)
  covalent geometry    : angle       0.97959 (24441)

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

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

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4358 Ramachandran restraints generated.
    2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.8490 (p0) cc_final: 0.8275 (p0)
REVERT: A  102 GLU cc_start: 0.8987 (tp30) cc_final: 0.8755 (tp30)
REVERT: A  119 LEU cc_start: 0.7162 (pp) cc_final: 0.6850 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1076
  time to fit residues: 4.8639
Evaluate side-chains
  29 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.133 
Evaluate side-chains
  38 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  261 MET cc_start: 0.5169 (ppp) cc_final: 0.4203 (pmm)
REVERT: B  273 LEU cc_start: 0.9591 (pp) cc_final: 0.9342 (tt)
REVERT: B  443 MET cc_start: 0.9447 (tpt) cc_final: 0.9097 (tpp)
REVERT: B  447 TRP cc_start: 0.8910 (p-90) cc_final: 0.8646 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1476
  time to fit residues: 7.9873
Evaluate side-chains
  32 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 174 optimal weight:    0.0060
   chunk 186 optimal weight:    0.0060
   chunk 58 optimal weight:    4.9990
   chunk 211 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 27 optimal weight:    0.3980
   chunk 215 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 196 optimal weight:    0.0020
   chunk 103 optimal weight:    0.0980
   overall best weight:    0.1020
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.050889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.037850 restraints weight = 6650.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.039542 restraints weight = 4576.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.040889 restraints weight = 3444.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.2867
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.077647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.061637 restraints weight = 31231.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.063192 restraints weight = 26131.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.063305 restraints weight = 11229.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6483
moved from start:          1.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  17955  Z= 0.214
  Angle     :  0.980  31.480  24483  Z= 0.492
  Chirality :  0.058   0.422   2799
  Planarity :  0.008   0.052   3078
  Dihedral  :  5.689  25.068   2367
  Min Nonbonded Distance : 1.728

Molprobity Statistics.
  All-atom Clashscore : 19.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.50 (0.18), residues: 2181
  helix: -0.81 (0.28), residues: 318
  sheet:  0.18 (0.16), residues: 900
  loop : -0.53 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.005   TRP F 447 
 HIS   0.021   0.004   HIS F 478 
 PHE   0.016   0.003   PHE C  62 
 TYR   0.058   0.006   TYR A 140 
 ARG   0.031   0.002   ARG A  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 (  743)
  hydrogen bonds       : angle       6.47234 ( 2076)
  SS BOND              : bond        0.00487 (   21)
  SS BOND              : angle       1.11723 (   42)
  covalent geometry    : bond        0.00494 (17934)
  covalent geometry    : angle       0.97959 (24441)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3500.10 seconds
wall clock time: 63 minutes 15.43 seconds (3795.43 seconds total)