Starting phenix.real_space_refine
on Wed Mar 12 10:15:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jh5_36254/03_2025/8jh5_36254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jh5_36254/03_2025/8jh5_36254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jh5_36254/03_2025/8jh5_36254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jh5_36254/03_2025/8jh5_36254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jh5_36254/03_2025/8jh5_36254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jh5_36254/03_2025/8jh5_36254.cif"
  }
  resolution = 3.7
  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=   0.003 sd=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5070      2.51       5
     N    1266      2.21       5
     O    1342      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7734
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2957
          Classifications: {'peptide': 379}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 360}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 893
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'NPS': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    D, B
  Time building chain proxies: 6.25, per 1000 atoms: 0.81
  Number of scatterers: 7734
  At special positions: 0
  Unit cell: (106.7, 121, 96.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1342      8.00
     N    1266      7.00
     C    5070      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D 100 " 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: 1.92
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      48.6% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 13
      removed outlier: 4.149A  pdb=" N   PHE A   7 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET A  11 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA A  13 " --> pdb=" O   HIS A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 30
      removed outlier: 3.532A  pdb=" N   TYR A  18 " --> pdb=" O   MET A  14 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ALA A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   VAL A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A  29 " --> pdb=" O   TYR A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 49
      removed outlier: 4.120A  pdb=" N   ILE A  42 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN A  43 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A  47 " --> pdb=" O   ASN A  43 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 60
      removed outlier: 3.597A  pdb=" N   LEU A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   HIS A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 90
      removed outlier: 4.010A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 3.505A  pdb=" N   LEU A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 133
    Processing helix  chain 'A' and resid 133 through 141
      removed outlier: 3.764A  pdb=" N   VAL A 137 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 3.557A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 474
      removed outlier: 3.565A  pdb=" N   THR A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ARG A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TRP A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   LYS A 472 " --> pdb=" O   MET A 468 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 474 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.929A  pdb=" N   PHE A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   LYS A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TRP A 495 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
      removed outlier: 3.589A  pdb=" N   SER A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 529
      removed outlier: 3.556A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 524 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A 527 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN A 529 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 544
      removed outlier: 3.657A  pdb=" N   ALA A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 556
      removed outlier: 3.690A  pdb=" N   VAL A 554 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 575
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.636A  pdb=" N   ALA A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU A 590 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 608
      removed outlier: 4.022A  pdb=" N   LEU A 598 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 607 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 621
      removed outlier: 4.348A  pdb=" N   LEU A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A 621 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 13
      removed outlier: 4.148A  pdb=" N   PHE B   7 " --> pdb=" O   THR B   3 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET B  11 " --> pdb=" O   PHE B   7 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA B  13 " --> pdb=" O   HIS B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 30
      removed outlier: 3.533A  pdb=" N   TYR B  18 " --> pdb=" O   MET B  14 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA B  20 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ALA B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 49
      removed outlier: 4.120A  pdb=" N   ILE B  42 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN B  43 " --> pdb=" O   CYS B  39 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA B  47 " --> pdb=" O   ASN B  43 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B  48 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 60
      removed outlier: 3.597A  pdb=" N   LEU B  53 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   HIS B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 90
      removed outlier: 4.009A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 116 through 123
      removed outlier: 3.505A  pdb=" N   LEU B 120 " --> pdb=" O   MET B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 133
    Processing helix  chain 'B' and resid 133 through 141
      removed outlier: 3.764A  pdb=" N   VAL B 137 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 165
      removed outlier: 3.558A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLN B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 474
      removed outlier: 3.566A  pdb=" N   THR B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   ARG B 463 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU B 466 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TRP B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   LYS B 472 " --> pdb=" O   MET B 468 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 474 " --> pdb=" O   TRP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 479
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.929A  pdb=" N   PHE B 484 " --> pdb=" O   TYR B 480 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 486 " --> pdb=" O   SER B 482 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE B 493 " --> pdb=" O   SER B 489 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   LYS B 494 " --> pdb=" O   LEU B 490 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP B 495 " --> pdb=" O   ILE B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 508
      removed outlier: 3.589A  pdb=" N   SER B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 529
      removed outlier: 3.556A  pdb=" N   MET B 519 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 524 " --> pdb=" O   PHE B 520 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET B 526 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ALA B 527 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU B 528 " --> pdb=" O   LEU B 524 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN B 529 " --> pdb=" O   PHE B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 544
      removed outlier: 3.657A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 556
      removed outlier: 3.689A  pdb=" N   VAL B 554 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET B 555 " --> pdb=" O   GLY B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 575
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.636A  pdb=" N   ALA B 588 " --> pdb=" O   PRO B 584 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU B 590 " --> pdb=" O   VAL B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 608
      removed outlier: 4.022A  pdb=" N   LEU B 598 " --> pdb=" O   HIS B 594 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE B 603 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE B 608 " --> pdb=" O   PHE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 621
      removed outlier: 4.348A  pdb=" N   LEU B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11
      removed outlier: 3.563A  pdb=" N   GLN C   7 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 16
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 56
      removed outlier: 6.623A  pdb=" N   TRP C  40 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   ALA C  54 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   MET C  38 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR C  41 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR C  99 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 11
      removed outlier: 3.563A  pdb=" N   GLN D   7 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 15 through 16
    Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 56
      removed outlier: 6.623A  pdb=" N   TRP D  40 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   ALA D  54 " --> pdb=" O   MET D  38 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET D  38 " --> pdb=" O   ALA D  54 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 109
      removed outlier: 6.534A  pdb=" N   TRP D 107 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)

    257 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1178
        1.30 -     1.43: 2126
        1.43 -     1.55: 4515
        1.55 -     1.68: 3
        1.68 -     1.81: 100
  Bond restraints: 7922
  Sorted by residual:
  bond pdb=" CA  ASN A 112 "
       pdb=" C   ASN A 112 "
    ideal  model  delta    sigma   weight residual
    1.526  1.438  0.087 1.30e-02 5.92e+03 4.52e+01
  bond pdb=" CA  ASN B 112 "
       pdb=" C   ASN B 112 "
    ideal  model  delta    sigma   weight residual
    1.526  1.438  0.087 1.30e-02 5.92e+03 4.52e+01
  bond pdb=" CA  PHE A 585 "
       pdb=" C   PHE A 585 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.082 1.37e-02 5.33e+03 3.55e+01
  bond pdb=" CA  PHE B 585 "
       pdb=" C   PHE B 585 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.081 1.37e-02 5.33e+03 3.46e+01
  bond pdb=" C   PHE B 585 "
       pdb=" O   PHE B 585 "
    ideal  model  delta    sigma   weight residual
    1.236  1.168  0.068 1.28e-02 6.10e+03 2.82e+01
  ... (remaining 7917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.60: 10722
        4.60 -     9.21: 44
        9.21 -    13.81: 2
       13.81 -    18.41: 0
       18.41 -    23.02: 4
  Bond angle restraints: 10772
  Sorted by residual:
  angle pdb=" O   NPS A 701 "
        pdb=" C15 NPS A 701 "
        pdb=" OXT NPS A 701 "
      ideal   model   delta    sigma   weight residual
     126.82  103.80   23.02 3.00e+00 1.11e-01 5.89e+01
  angle pdb=" O   NPS B 701 "
        pdb=" C15 NPS B 701 "
        pdb=" OXT NPS B 701 "
      ideal   model   delta    sigma   weight residual
     126.82  103.82   23.00 3.00e+00 1.11e-01 5.88e+01
  angle pdb=" O   NPS B 701 "
        pdb=" C15 NPS B 701 "
        pdb=" C14 NPS B 701 "
      ideal   model   delta    sigma   weight residual
     116.41  138.94  -22.53 3.00e+00 1.11e-01 5.64e+01
  angle pdb=" O   NPS A 701 "
        pdb=" C15 NPS A 701 "
        pdb=" C14 NPS A 701 "
      ideal   model   delta    sigma   weight residual
     116.41  138.92  -22.51 3.00e+00 1.11e-01 5.63e+01
  angle pdb=" N   PHE A 585 "
        pdb=" CA  PHE A 585 "
        pdb=" C   PHE A 585 "
      ideal   model   delta    sigma   weight residual
     112.45  104.66    7.79 1.39e+00 5.18e-01 3.14e+01
  ... (remaining 10767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.88: 4440
       14.88 -    29.76: 147
       29.76 -    44.64: 71
       44.64 -    59.51: 6
       59.51 -    74.39: 2
  Dihedral angle restraints: 4666
    sinusoidal: 1806
      harmonic: 2860
  Sorted by residual:
  dihedral pdb=" CA  ILE D  35 "
           pdb=" C   ILE D  35 "
           pdb=" N   THR D  36 "
           pdb=" CA  THR D  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.45  -38.55     0      5.00e+00 4.00e-02 5.95e+01
  dihedral pdb=" CA  ILE C  35 "
           pdb=" C   ILE C  35 "
           pdb=" N   THR C  36 "
           pdb=" CA  THR C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.46  -38.54     0      5.00e+00 4.00e-02 5.94e+01
  dihedral pdb=" C   ASN B 112 "
           pdb=" N   ASN B 112 "
           pdb=" CA  ASN B 112 "
           pdb=" CB  ASN B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.35  -10.25     0      2.50e+00 1.60e-01 1.68e+01
  ... (remaining 4663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 614
       0.035 -    0.070: 446
       0.070 -    0.106: 123
       0.106 -    0.141: 43
       0.141 -    0.176: 20
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CB  VAL B 557 "
            pdb=" CA  VAL B 557 "
            pdb=" CG1 VAL B 557 "
            pdb=" CG2 VAL B 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CB  VAL A 557 "
            pdb=" CA  VAL A 557 "
            pdb=" CG1 VAL A 557 "
            pdb=" CG2 VAL A 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.63e-01
  chirality pdb=" CB  VAL D   6 "
            pdb=" CA  VAL D   6 "
            pdb=" CG1 VAL D   6 "
            pdb=" CG2 VAL D   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.62e-01
  ... (remaining 1243 not shown)

  Planarity restraints: 1320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 584 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.94e+00
        pdb=" C   PRO B 584 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   PRO B 584 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PHE B 585 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 584 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.93e+00
        pdb=" C   PRO A 584 "    0.049 2.00e-02 2.50e+03
        pdb=" O   PRO A 584 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE A 585 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 551 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO B 552 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 552 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 552 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1317 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2388
        2.84 -     3.35: 6505
        3.35 -     3.87: 11808
        3.87 -     4.38: 13316
        4.38 -     4.90: 23069
  Nonbonded interactions: 57086
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 547 "
            pdb=" O   ALA A 576 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" NH2 ARG B 547 "
            pdb=" O   ALA B 576 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" NH2 ARG D 101 "
            pdb=" OE2 GLU B 191 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" ND2 ASN B  43 "
            pdb=" OG  SER B 521 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" ND2 ASN A  43 "
            pdb=" OG  SER A 521 "
     model   vdw
     2.371 3.120
  ... (remaining 57081 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.210
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
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      :  0.006   0.090   7922  Z= 0.410
  Angle     :  0.965  23.015  10772  Z= 0.481
  Chirality :  0.053   0.176   1246
  Planarity :  0.007   0.053   1320
  Dihedral  :  9.929  74.392   2820
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -5.76 (0.20), residues: 976
  helix: -4.77 (0.08), residues: 512
  sheet: -1.41 (0.42), residues: 166
  loop : -2.85 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP C  37 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.022   0.002   PHE B 585 
 TYR   0.022   0.002   TYR C  56 
 ARG   0.003   0.001   ARG A 547 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8810 (t0) cc_final: 0.8567 (t0)
REVERT: A  196 ILE cc_start: 0.8605 (mt) cc_final: 0.8127 (mt)
REVERT: A  468 MET cc_start: 0.8521 (mmm) cc_final: 0.8308 (mmm)
REVERT: A  499 MET cc_start: 0.8561 (ttp) cc_final: 0.8353 (ttp)
REVERT: A  519 MET cc_start: 0.8565 (mmt) cc_final: 0.8362 (mmm)
REVERT: A  538 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7328 (tmt170)
REVERT: A  575 GLN cc_start: 0.8996 (pp30) cc_final: 0.8721 (pp30)
REVERT: A  599 SER cc_start: 0.9165 (p) cc_final: 0.8964 (p)
REVERT: A  615 LEU cc_start: 0.8924 (tp) cc_final: 0.8673 (tp)
REVERT: C   51 TRP cc_start: 0.7421 (m-10) cc_final: 0.7029 (m100)
REVERT: C   76 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6818 (ttp-110)
REVERT: D   42 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8426 (ptm160)
REVERT: D   76 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6552 (ttp-170)
REVERT: B   62 ASN cc_start: 0.8811 (t0) cc_final: 0.8568 (t0)
REVERT: B  196 ILE cc_start: 0.8627 (mt) cc_final: 0.8156 (mt)
REVERT: B  468 MET cc_start: 0.8523 (mmm) cc_final: 0.8295 (mmm)
REVERT: B  499 MET cc_start: 0.8558 (ttp) cc_final: 0.8351 (ttp)
REVERT: B  519 MET cc_start: 0.8552 (mmt) cc_final: 0.8292 (mmm)
REVERT: B  615 LEU cc_start: 0.8936 (tp) cc_final: 0.8690 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2991
  time to fit residues: 87.9416
Evaluate side-chains
  157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:   40.0000
   chunk 38 optimal weight:   50.0000
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:   30.0000
   chunk 56 optimal weight:    9.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A   9 HIS
A  43 ASN
** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 HIS
C   7 GLN
B   9 HIS
B  43 ASN
B 127 ASN
** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 570 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.146410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.098594 restraints weight = 12446.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.101598 restraints weight = 6587.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.103591 restraints weight = 4436.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7922  Z= 0.376
  Angle     :  0.707   6.518  10772  Z= 0.366
  Chirality :  0.046   0.124   1246
  Planarity :  0.006   0.048   1320
  Dihedral  :  5.768  34.425   1084
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 10.75 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -4.66 (0.22), residues: 976
  helix: -3.51 (0.14), residues: 502
  sheet: -0.85 (0.44), residues: 158
  loop : -3.18 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 144 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.027   0.002   PHE A 128 
 TYR   0.027   0.001   TYR C  56 
 ARG   0.007   0.001   ARG B 463 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.7379 (tp30) cc_final: 0.6879 (tm-30)
REVERT: A  196 ILE cc_start: 0.8488 (mt) cc_final: 0.7763 (mt)
REVERT: A  468 MET cc_start: 0.8837 (mmm) cc_final: 0.8424 (mmm)
REVERT: A  519 MET cc_start: 0.8693 (mmt) cc_final: 0.8466 (mmm)
REVERT: A  538 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7208 (tmt170)
REVERT: C   51 TRP cc_start: 0.7354 (m-10) cc_final: 0.6993 (m100)
REVERT: C   76 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.6556 (ttm110)
REVERT: C  107 TRP cc_start: 0.7694 (m100) cc_final: 0.7427 (m100)
REVERT: D   42 ARG cc_start: 0.8680 (ptp-110) cc_final: 0.8385 (ptp-110)
REVERT: D   76 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.6415 (ttp-170)
REVERT: B  195 GLU cc_start: 0.7295 (tp30) cc_final: 0.7075 (tm-30)
REVERT: B  196 ILE cc_start: 0.8471 (mt) cc_final: 0.7988 (mt)
REVERT: B  468 MET cc_start: 0.8841 (mmm) cc_final: 0.8428 (mmm)
REVERT: B  517 MET cc_start: 0.8029 (mmm) cc_final: 0.7687 (ttm)
REVERT: B  519 MET cc_start: 0.8626 (mmt) cc_final: 0.8422 (mmm)
REVERT: B  538 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7274 (tmt170)
  outliers start: 30
  outliers final: 20
  residues processed: 202
  average time/residue: 0.2231
  time to fit residues: 59.3551
Evaluate side-chains
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.150051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102164 restraints weight = 12486.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.105294 restraints weight = 6521.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.107398 restraints weight = 4343.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7922  Z= 0.169
  Angle     :  0.578   7.348  10772  Z= 0.292
  Chirality :  0.042   0.135   1246
  Planarity :  0.005   0.036   1320
  Dihedral  :  5.092  32.187   1084
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.89 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.32 (0.24), residues: 976
  helix: -2.30 (0.19), residues: 500
  sheet:  0.83 (0.53), residues: 100
  loop : -2.77 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.002   0.000   HIS A 203 
 PHE   0.020   0.001   PHE A 128 
 TYR   0.022   0.001   TYR C  56 
 ARG   0.005   0.001   ARG C  71 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8742 (p)
REVERT: A  196 ILE cc_start: 0.8518 (mt) cc_final: 0.8184 (mt)
REVERT: A  468 MET cc_start: 0.8845 (mmm) cc_final: 0.8295 (mmm)
REVERT: A  517 MET cc_start: 0.7835 (mmm) cc_final: 0.7432 (ttm)
REVERT: A  538 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7296 (tmt170)
REVERT: A  616 TYR cc_start: 0.8355 (m-80) cc_final: 0.7964 (m-80)
REVERT: C   51 TRP cc_start: 0.7284 (m-10) cc_final: 0.6812 (m-90)
REVERT: C   76 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6634 (ttm170)
REVERT: C   87 MET cc_start: 0.8830 (mmm) cc_final: 0.8445 (mmp)
REVERT: D   42 ARG cc_start: 0.8641 (ptp-110) cc_final: 0.8420 (ptp-110)
REVERT: D   71 ARG cc_start: 0.5233 (ttp-110) cc_final: 0.4851 (ttp-170)
REVERT: D   76 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.5976 (ttp-110)
REVERT: B  145 TYR cc_start: 0.9118 (m-10) cc_final: 0.8835 (m-10)
REVERT: B  168 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8751 (p)
REVERT: B  196 ILE cc_start: 0.8531 (mt) cc_final: 0.8049 (mt)
REVERT: B  468 MET cc_start: 0.8841 (mmm) cc_final: 0.8222 (mmm)
REVERT: B  519 MET cc_start: 0.8569 (mmt) cc_final: 0.8356 (mmm)
REVERT: B  538 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7231 (tmt170)
REVERT: B  616 TYR cc_start: 0.8319 (m-80) cc_final: 0.7943 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 169
  average time/residue: 0.2327
  time to fit residues: 52.4213
Evaluate side-chains
  158 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0670
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.6722

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.150584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.102255 restraints weight = 12392.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.105372 restraints weight = 6475.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.107481 restraints weight = 4350.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7922  Z= 0.161
  Angle     :  0.564   8.338  10772  Z= 0.280
  Chirality :  0.042   0.145   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.818  31.040   1084
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.80 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.25), residues: 976
  helix: -1.58 (0.21), residues: 494
  sheet:  0.92 (0.52), residues: 100
  loop : -2.36 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 203 
 PHE   0.017   0.001   PHE A 128 
 TYR   0.024   0.001   TYR D  56 
 ARG   0.003   0.000   ARG A 463 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8644 (p)
REVERT: A  468 MET cc_start: 0.8864 (mmm) cc_final: 0.8609 (mmm)
REVERT: A  519 MET cc_start: 0.8696 (mmm) cc_final: 0.8447 (mmt)
REVERT: A  538 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7281 (tmt170)
REVERT: A  616 TYR cc_start: 0.8428 (m-80) cc_final: 0.8149 (m-80)
REVERT: C   51 TRP cc_start: 0.7159 (m-10) cc_final: 0.6759 (m-90)
REVERT: D   41 TYR cc_start: 0.7701 (p90) cc_final: 0.6735 (p90)
REVERT: D   42 ARG cc_start: 0.8527 (ptp-110) cc_final: 0.8215 (ptm160)
REVERT: B  145 TYR cc_start: 0.9135 (m-10) cc_final: 0.8867 (m-10)
REVERT: B  168 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8653 (p)
REVERT: B  195 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6444 (tm-30)
REVERT: B  196 ILE cc_start: 0.8258 (mt) cc_final: 0.8017 (mt)
REVERT: B  468 MET cc_start: 0.8842 (mmm) cc_final: 0.8574 (mmm)
REVERT: B  538 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7230 (tmt170)
REVERT: B  616 TYR cc_start: 0.8343 (m-80) cc_final: 0.8082 (m-80)
  outliers start: 25
  outliers final: 20
  residues processed: 171
  average time/residue: 0.3391
  time to fit residues: 77.7388
Evaluate side-chains
  163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   72 PHE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 44 optimal weight:   30.0000
   chunk 86 optimal weight:    0.0870
   chunk 82 optimal weight:    0.4980
   chunk 50 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    0.1980
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.3760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.152423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.104107 restraints weight = 12366.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.107356 restraints weight = 6457.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.109299 restraints weight = 4321.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7922  Z= 0.134
  Angle     :  0.556   7.951  10772  Z= 0.273
  Chirality :  0.041   0.135   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.522  29.565   1084
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.53 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.26), residues: 976
  helix: -0.97 (0.22), residues: 490
  sheet: -0.09 (0.45), residues: 142
  loop : -2.10 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 570 
 PHE   0.016   0.001   PHE C  72 
 TYR   0.024   0.001   TYR C  56 
 ARG   0.003   0.000   ARG D  71 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8551 (p)
REVERT: A  195 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6430 (tm-30)
REVERT: A  196 ILE cc_start: 0.8577 (mt) cc_final: 0.8350 (mp)
REVERT: A  538 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7301 (tmt170)
REVERT: C   51 TRP cc_start: 0.7047 (m-10) cc_final: 0.6714 (m-90)
REVERT: C   87 MET cc_start: 0.7811 (mmm) cc_final: 0.7589 (mmm)
REVERT: D   41 TYR cc_start: 0.7601 (p90) cc_final: 0.6684 (p90)
REVERT: D   42 ARG cc_start: 0.8422 (ptp-110) cc_final: 0.8031 (ptm160)
REVERT: D   76 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.6993 (ttm170)
REVERT: B  168 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8551 (p)
REVERT: B  195 GLU cc_start: 0.6578 (tm-30) cc_final: 0.6331 (tm-30)
REVERT: B  517 MET cc_start: 0.7914 (mmm) cc_final: 0.7438 (ttm)
REVERT: B  538 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7229 (tmt170)
  outliers start: 24
  outliers final: 15
  residues processed: 166
  average time/residue: 0.2102
  time to fit residues: 46.0319
Evaluate side-chains
  157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.150587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.102482 restraints weight = 12292.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.105563 restraints weight = 6446.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.107644 restraints weight = 4316.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7922  Z= 0.189
  Angle     :  0.565   8.018  10772  Z= 0.277
  Chirality :  0.042   0.128   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.525  29.092   1084
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.61 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.27), residues: 976
  helix: -0.63 (0.23), residues: 488
  sheet: -0.06 (0.46), residues: 140
  loop : -2.02 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.014   0.001   PHE A 128 
 TYR   0.025   0.001   TYR C  56 
 ARG   0.002   0.000   ARG A 471 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8636 (p)
REVERT: A  195 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6765 (tm-30)
REVERT: A  517 MET cc_start: 0.7767 (mmm) cc_final: 0.7337 (ttm)
REVERT: A  538 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7284 (tmt170)
REVERT: C   51 TRP cc_start: 0.7027 (m-10) cc_final: 0.6736 (m-90)
REVERT: D   41 TYR cc_start: 0.7482 (p90) cc_final: 0.6585 (p90)
REVERT: D   42 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.8020 (ptm160)
REVERT: B  145 TYR cc_start: 0.9112 (m-10) cc_final: 0.8908 (m-10)
REVERT: B  168 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8631 (p)
REVERT: B  517 MET cc_start: 0.7984 (mmm) cc_final: 0.7468 (ttm)
REVERT: B  538 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7222 (tmt170)
  outliers start: 27
  outliers final: 23
  residues processed: 162
  average time/residue: 0.2245
  time to fit residues: 49.7800
Evaluate side-chains
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 26 optimal weight:    0.1980
   chunk 90 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.149774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.100574 restraints weight = 12488.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.103671 restraints weight = 6583.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.105794 restraints weight = 4461.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7922  Z= 0.206
  Angle     :  0.583   9.325  10772  Z= 0.285
  Chirality :  0.043   0.145   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.572  28.486   1084
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.10 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.27), residues: 976
  helix: -0.45 (0.23), residues: 488
  sheet: -0.03 (0.46), residues: 140
  loop : -1.94 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.014   0.001   PHE A 128 
 TYR   0.021   0.001   TYR C  56 
 ARG   0.002   0.000   ARG A 471 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A   11 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8354 (mpp)
REVERT: A  168 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8613 (p)
REVERT: A  195 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6872 (tm-30)
REVERT: A  517 MET cc_start: 0.7760 (mmm) cc_final: 0.7463 (ttm)
REVERT: A  538 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7225 (tmt170)
REVERT: C   51 TRP cc_start: 0.6987 (m-10) cc_final: 0.6695 (m-90)
REVERT: D   41 TYR cc_start: 0.7426 (p90) cc_final: 0.6073 (p90)
REVERT: D   42 ARG cc_start: 0.8381 (ptp-110) cc_final: 0.7945 (ptm160)
REVERT: D   49 ARG cc_start: 0.8229 (ptp-170) cc_final: 0.7935 (ptm160)
REVERT: D   87 MET cc_start: 0.7953 (mmm) cc_final: 0.7368 (mmm)
REVERT: B  168 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8614 (p)
REVERT: B  517 MET cc_start: 0.7921 (mmm) cc_final: 0.7335 (ttm)
REVERT: B  538 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7206 (tmt170)
  outliers start: 30
  outliers final: 23
  residues processed: 165
  average time/residue: 0.1913
  time to fit residues: 42.6622
Evaluate side-chains
  165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0870
   chunk 80 optimal weight:    0.0670
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5296

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

Flipped N/Q/H residues before XYZ refinement:
B 575 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.152266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.104061 restraints weight = 12526.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.107254 restraints weight = 6442.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.109376 restraints weight = 4303.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7922  Z= 0.141
  Angle     :  0.561   8.839  10772  Z= 0.274
  Chirality :  0.042   0.142   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.359  28.886   1084
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.43 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.28), residues: 976
  helix: -0.10 (0.24), residues: 486
  sheet:  0.14 (0.47), residues: 140
  loop : -1.68 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.031   0.001   PHE A   7 
 TYR   0.018   0.001   TYR D  56 
 ARG   0.003   0.000   ARG C  49 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8403 (p)
REVERT: A  517 MET cc_start: 0.7734 (mmm) cc_final: 0.7417 (ttm)
REVERT: A  538 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7205 (tmt170)
REVERT: C   51 TRP cc_start: 0.6885 (m-10) cc_final: 0.6656 (m-90)
REVERT: C  103 LYS cc_start: 0.7184 (tttt) cc_final: 0.6905 (ptmm)
REVERT: D   41 TYR cc_start: 0.7343 (p90) cc_final: 0.6047 (p90)
REVERT: D   42 ARG cc_start: 0.8363 (ptp-110) cc_final: 0.7930 (ptm160)
REVERT: D   49 ARG cc_start: 0.8288 (ptp-170) cc_final: 0.8035 (ptm160)
REVERT: D   87 MET cc_start: 0.8143 (mmm) cc_final: 0.7907 (mmm)
REVERT: B  168 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8407 (p)
REVERT: B  195 GLU cc_start: 0.6522 (tm-30) cc_final: 0.6230 (tm-30)
REVERT: B  517 MET cc_start: 0.7925 (mmm) cc_final: 0.7274 (ttm)
REVERT: B  538 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7217 (tmt170)
  outliers start: 23
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1908
  time to fit residues: 42.6439
Evaluate side-chains
  165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.151368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.102162 restraints weight = 12620.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.105314 restraints weight = 6577.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.107471 restraints weight = 4419.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7922  Z= 0.155
  Angle     :  0.562   9.548  10772  Z= 0.273
  Chirality :  0.042   0.163   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.356  28.705   1084
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.55 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.28), residues: 976
  helix:  0.12 (0.25), residues: 484
  sheet:  0.29 (0.47), residues: 140
  loop : -1.65 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.020   0.001   PHE A   7 
 TYR   0.018   0.001   TYR D  56 
 ARG   0.002   0.000   ARG A 187 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8452 (p)
REVERT: A  517 MET cc_start: 0.7737 (mmm) cc_final: 0.7395 (ttm)
REVERT: A  538 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7245 (tmt170)
REVERT: C   51 TRP cc_start: 0.6818 (m-10) cc_final: 0.6548 (m-90)
REVERT: C  103 LYS cc_start: 0.7156 (tttt) cc_final: 0.6937 (ptmm)
REVERT: B  168 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8446 (p)
REVERT: B  195 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6222 (tm-30)
REVERT: B  517 MET cc_start: 0.7935 (mmm) cc_final: 0.7299 (ttm)
REVERT: B  538 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7256 (tmt170)
  outliers start: 24
  outliers final: 21
  residues processed: 164
  average time/residue: 0.1974
  time to fit residues: 43.7943
Evaluate side-chains
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 85 optimal weight:    0.4980
   chunk 94 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 7 optimal weight:    0.5980
   chunk 81 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.152035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.102375 restraints weight = 12605.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.105554 restraints weight = 6586.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.107620 restraints weight = 4435.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7922  Z= 0.145
  Angle     :  0.567   9.899  10772  Z= 0.275
  Chirality :  0.042   0.184   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.321  27.784   1084
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.79 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.28), residues: 976
  helix:  0.28 (0.25), residues: 482
  sheet:  0.40 (0.48), residues: 140
  loop : -1.56 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.021   0.001   PHE A   7 
 TYR   0.018   0.001   TYR D  56 
 ARG   0.007   0.000   ARG C  71 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8416 (p)
REVERT: A  517 MET cc_start: 0.7742 (mmm) cc_final: 0.7450 (ttm)
REVERT: A  538 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7260 (tmt170)
REVERT: C   49 ARG cc_start: 0.8576 (ptp-170) cc_final: 0.8174 (ptm160)
REVERT: C   51 TRP cc_start: 0.6652 (m-10) cc_final: 0.6421 (m-90)
REVERT: C   87 MET cc_start: 0.8073 (mmm) cc_final: 0.7407 (mmm)
REVERT: D   41 TYR cc_start: 0.7400 (p90) cc_final: 0.6516 (p90)
REVERT: B  168 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8411 (p)
REVERT: B  195 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6184 (tm-30)
REVERT: B  517 MET cc_start: 0.7920 (mmm) cc_final: 0.7239 (ttm)
REVERT: B  538 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7255 (tmt170)
  outliers start: 24
  outliers final: 21
  residues processed: 167
  average time/residue: 0.1845
  time to fit residues: 42.0039
Evaluate side-chains
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 90 optimal weight:    0.8980
   chunk 38 optimal weight:   20.0000
   chunk 10 optimal weight:    0.0970
   chunk 31 optimal weight:    0.0970
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.2180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.149258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.100576 restraints weight = 12650.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.103751 restraints weight = 6728.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.105320 restraints weight = 4443.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7922  Z= 0.229
  Angle     :  0.599   9.677  10772  Z= 0.292
  Chirality :  0.044   0.151   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.502  27.961   1084
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.15 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.28), residues: 976
  helix:  0.16 (0.24), residues: 484
  sheet:  0.07 (0.45), residues: 162
  loop : -1.57 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  37 
 HIS   0.001   0.001   HIS B 176 
 PHE   0.021   0.001   PHE A   7 
 TYR   0.022   0.001   TYR C  56 
 ARG   0.003   0.000   ARG C  71 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2813.50 seconds
wall clock time: 51 minutes 20.30 seconds (3080.30 seconds total)