Starting phenix.real_space_refine
on Sat Dec 28 04:42:34 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y9u_33692/12_2024/7y9u_33692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y9u_33692/12_2024/7y9u_33692.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y9u_33692/12_2024/7y9u_33692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y9u_33692/12_2024/7y9u_33692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y9u_33692/12_2024/7y9u_33692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y9u_33692/12_2024/7y9u_33692.cif"
  }
  resolution = 3.3
  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=   0.004 sd=   0.116
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    5078      2.51       5
     N    1272      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 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 7748
  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: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 895
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'E7O': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 5.84, per 1000 atoms: 0.75
  Number of scatterers: 7748
  At special positions: 0
  Unit cell: (100.1, 123.2, 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    1272      7.00
     C    5078      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C 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: 1.95
  Conformation dependent library (CDL) restraints added in 1.1 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:
      44 helices and 8 sheets defined
      51.6% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 30
      removed outlier: 3.846A  pdb=" N   PHE A   7 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A  13 " --> pdb=" O   HIS A   9 " (cutoff:3.500A)
      Proline residue:  A  16  - end of helix
      removed outlier: 4.041A  pdb=" N   ALA A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET A  21 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 49
      removed outlier: 3.886A  pdb=" N   ASN A  43 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 60
      removed outlier: 3.874A  pdb=" N   PHE A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 76
      removed outlier: 3.523A  pdb=" N   ALA A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 70 through 76'
    Processing helix  chain 'A' and resid 77 through 86
      removed outlier: 4.120A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.662A  pdb=" N   LYS A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.510A  pdb=" N   ILE A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 110 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 126
    Processing helix  chain 'A' and resid 128 through 143
      removed outlier: 3.933A  pdb=" N   VAL A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN A 135 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 3.664A  pdb=" N   LEU A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 457 through 474
      removed outlier: 3.751A  pdb=" N   THR A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ARG A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A 472 " --> pdb=" O   MET A 468 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 474 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 480
      removed outlier: 3.535A  pdb=" N   SER A 479 " --> pdb=" O   ASN A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 493
      removed outlier: 3.563A  pdb=" N   TRP A 488 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 491 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
    Processing helix  chain 'A' and resid 510 through 512
      No H-bonds generated for 'chain 'A' and resid 510 through 512'
    Processing helix  chain 'A' and resid 513 through 529
      removed outlier: 3.531A  pdb=" N   MET A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY A 523 " --> pdb=" O   MET A 519 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   MET A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 527 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASN A 529 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.541A  pdb=" N   ALA A 541 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.710A  pdb=" N   HIS A 570 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 574 " --> pdb=" O   HIS A 570 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.558A  pdb=" N   ALA A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 590 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 608
      removed outlier: 3.529A  pdb=" N   ALA A 601 " --> pdb=" O   ILE A 597 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL A 602 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 622
      removed outlier: 3.820A  pdb=" N   LEU A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A 621 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 30
      removed outlier: 3.846A  pdb=" N   PHE B   7 " --> pdb=" O   THR B   3 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR B   8 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA B  13 " --> pdb=" O   HIS B   9 " (cutoff:3.500A)
      Proline residue:  B  16  - end of helix
      removed outlier: 4.041A  pdb=" N   ALA B  20 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 49
      removed outlier: 3.886A  pdb=" N   ASN B  43 " --> pdb=" O   CYS B  39 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B  48 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 60
      removed outlier: 3.874A  pdb=" N   PHE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 76
      removed outlier: 3.522A  pdb=" N   ALA B  74 " --> pdb=" O   ARG B  70 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP B  75 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 70 through 76'
    Processing helix  chain 'B' and resid 77 through 86
      removed outlier: 4.120A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.662A  pdb=" N   LYS B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 110
      removed outlier: 3.510A  pdb=" N   ILE B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 110 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 126
    Processing helix  chain 'B' and resid 128 through 143
      removed outlier: 3.932A  pdb=" N   VAL B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN B 135 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 165
      removed outlier: 3.663A  pdb=" N   LEU B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 457 through 474
      removed outlier: 3.752A  pdb=" N   THR B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ARG B 463 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU B 466 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS B 472 " --> pdb=" O   MET B 468 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B 474 " --> pdb=" O   TRP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 480
      removed outlier: 3.534A  pdb=" N   SER B 479 " --> pdb=" O   ASN B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 3.563A  pdb=" N   TRP B 488 " --> pdb=" O   PHE B 484 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE B 491 " --> pdb=" O   THR B 487 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE B 493 " --> pdb=" O   SER B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 508
    Processing helix  chain 'B' and resid 510 through 512
      No H-bonds generated for 'chain 'B' and resid 510 through 512'
    Processing helix  chain 'B' and resid 513 through 529
      removed outlier: 3.532A  pdb=" N   MET B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   MET B 519 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B 523 " --> pdb=" O   MET B 519 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   MET B 526 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 527 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN B 529 " --> pdb=" O   PHE B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 542
      removed outlier: 3.541A  pdb=" N   ALA B 541 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 577
      removed outlier: 3.710A  pdb=" N   HIS B 570 " --> pdb=" O   GLY B 566 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA B 572 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 574 " --> pdb=" O   HIS B 570 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA B 576 " --> pdb=" O   ALA B 572 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.558A  pdb=" N   ALA B 588 " --> pdb=" O   PRO B 584 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU B 590 " --> pdb=" O   VAL B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 608
      removed outlier: 3.529A  pdb=" N   ALA B 601 " --> pdb=" O   ILE B 597 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL B 602 " --> pdb=" O   LEU B 598 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE B 603 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE B 608 " --> pdb=" O   PHE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 622
      removed outlier: 3.820A  pdb=" N   LEU B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE B 618 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177
      removed outlier: 7.381A  pdb=" N   VAL A 204 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE A 175 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 206 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL A 177 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR C 107 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C  97 " --> pdb=" O   GLN C  43 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR C  99 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR C  41 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG C 101 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLU C  39 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   TRP C  40 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11
      removed outlier: 3.630A  pdb=" N   GLN C   7 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER C  29 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16
      removed outlier: 3.612A  pdb=" N   THR C 116 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 21 through 23
      removed outlier: 3.916A  pdb=" N   LEU C  22 " --> pdb=" O   MET C  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 11
      removed outlier: 3.630A  pdb=" N   GLN D   7 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER D  29 " --> pdb=" O   GLN D   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 14 through 16
      removed outlier: 3.613A  pdb=" N   THR D 116 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 23
      removed outlier: 3.915A  pdb=" N   LEU D  22 " --> pdb=" O   MET D  87 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 54
      removed outlier: 7.021A  pdb=" N   TRP D  40 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLU D  39 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG D 101 " --> pdb=" O   GLU D  39 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL D  97 " --> pdb=" O   GLN D  43 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TYR D 107 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ILE B 196 " --> pdb=" O   TYR D 107 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ARG D 109 " --> pdb=" O   ILE B 196 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL B 204 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ILE B 175 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL B 206 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL B 177 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)

    256 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: 2.94

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1184
        1.28 -     1.41: 2092
        1.41 -     1.54: 4528
        1.54 -     1.67: 32
        1.67 -     1.80: 100
  Bond restraints: 7936
  Sorted by residual:
  bond pdb=" CA  ASN A 112 "
       pdb=" C   ASN A 112 "
    ideal  model  delta    sigma   weight residual
    1.525  1.374  0.151 1.29e-02 6.01e+03 1.38e+02
  bond pdb=" CA  ASN B 112 "
       pdb=" C   ASN B 112 "
    ideal  model  delta    sigma   weight residual
    1.525  1.374  0.151 1.29e-02 6.01e+03 1.37e+02
  bond pdb=" C04 E7O A 701 "
       pdb=" C05 E7O A 701 "
    ideal  model  delta    sigma   weight residual
    1.421  1.250  0.171 2.00e-02 2.50e+03 7.34e+01
  bond pdb=" C04 E7O B 701 "
       pdb=" C05 E7O B 701 "
    ideal  model  delta    sigma   weight residual
    1.421  1.250  0.171 2.00e-02 2.50e+03 7.29e+01
  bond pdb=" C04 E7O B 701 "
       pdb=" C10 E7O B 701 "
    ideal  model  delta    sigma   weight residual
    1.428  1.272  0.156 2.00e-02 2.50e+03 6.11e+01
  ... (remaining 7931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 10201
        2.12 -     4.24: 493
        4.24 -     6.37: 78
        6.37 -     8.49: 12
        8.49 -    10.61: 6
  Bond angle restraints: 10790
  Sorted by residual:
  angle pdb=" C   ASN B 112 "
        pdb=" CA  ASN B 112 "
        pdb=" CB  ASN B 112 "
      ideal   model   delta    sigma   weight residual
     111.31  100.98   10.33 1.68e+00 3.54e-01 3.78e+01
  angle pdb=" C   ASN A 112 "
        pdb=" CA  ASN A 112 "
        pdb=" CB  ASN A 112 "
      ideal   model   delta    sigma   weight residual
     111.31  100.99   10.32 1.68e+00 3.54e-01 3.77e+01
  angle pdb=" C   GLN D  56 "
        pdb=" N   SER D  57 "
        pdb=" CA  SER D  57 "
      ideal   model   delta    sigma   weight residual
     121.19  127.35   -6.16 1.59e+00 3.96e-01 1.50e+01
  angle pdb=" C   GLN C  56 "
        pdb=" N   SER C  57 "
        pdb=" CA  SER C  57 "
      ideal   model   delta    sigma   weight residual
     121.19  127.34   -6.15 1.59e+00 3.96e-01 1.50e+01
  angle pdb=" C   PRO B 111 "
        pdb=" N   ASN B 112 "
        pdb=" CA  ASN B 112 "
      ideal   model   delta    sigma   weight residual
     122.85  128.12   -5.27 1.39e+00 5.18e-01 1.44e+01
  ... (remaining 10785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.31: 4415
       15.31 -    30.61: 189
       30.61 -    45.92: 53
       45.92 -    61.23: 6
       61.23 -    76.54: 2
  Dihedral angle restraints: 4665
    sinusoidal: 1803
      harmonic: 2862
  Sorted by residual:
  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 -107.69  -14.91     0      2.50e+00 1.60e-01 3.56e+01
  dihedral pdb=" C   ASN A 112 "
           pdb=" N   ASN A 112 "
           pdb=" CA  ASN A 112 "
           pdb=" CB  ASN A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.70  -14.90     0      2.50e+00 1.60e-01 3.55e+01
  dihedral pdb=" CA  GLN C  56 "
           pdb=" C   GLN C  56 "
           pdb=" N   SER C  57 "
           pdb=" CA  SER C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.54  -28.46     0      5.00e+00 4.00e-02 3.24e+01
  ... (remaining 4662 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 984
       0.069 -    0.137: 239
       0.137 -    0.206: 17
       0.206 -    0.275: 4
       0.275 -    0.343: 2
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CB  ILE C  55 "
            pdb=" CA  ILE C  55 "
            pdb=" CG1 ILE C  55 "
            pdb=" CG2 ILE C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CB  ILE D  55 "
            pdb=" CA  ILE D  55 "
            pdb=" CG1 ILE D  55 "
            pdb=" CG2 ILE D  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CB  VAL B 554 "
            pdb=" CA  VAL B 554 "
            pdb=" CG1 VAL B 554 "
            pdb=" CG2 VAL B 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1243 not shown)

  Planarity restraints: 1326
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 551 "   -0.045 5.00e-02 4.00e+02   6.79e-02 7.37e+00
        pdb=" N   PRO A 552 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 552 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 552 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 551 "    0.045 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO B 552 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 552 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 552 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  15 "   -0.041 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO B  16 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1323 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 41
        2.61 -     3.18: 5951
        3.18 -     3.75: 10860
        3.75 -     4.33: 15633
        4.33 -     4.90: 25609
  Nonbonded interactions: 58094
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D  26 "
            pdb=" SG  CYS D 100 "
     model   vdw
     2.034 3.760
  nonbonded pdb=" OE2 GLU A 193 "
            pdb=" NE  ARG C 109 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" OE2 GLU A 191 "
            pdb=" NH2 ARG C 101 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NH2 ARG C  71 "
            pdb=" O   SER C  89 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" NH2 ARG D  71 "
            pdb=" O   SER D  89 "
     model   vdw
     2.352 3.120
  ... (remaining 58089 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.470
  Find NCS groups from input model:        0.400
  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:3.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
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      :  0.011   0.171   7936  Z= 0.717
  Angle     :  1.056  10.612  10790  Z= 0.561
  Chirality :  0.060   0.343   1246
  Planarity :  0.009   0.068   1326
  Dihedral  : 10.083  76.536   2822
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.22 %
  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: -6.23 (0.17), residues: 976
  helix: -4.89 (0.07), residues: 524
  sheet: -2.72 (0.40), residues: 106
  loop : -2.86 (0.27), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B  31 
 HIS   0.009   0.003   HIS A   9 
 PHE   0.022   0.003   PHE A 587 
 TYR   0.016   0.002   TYR C  41 
 ARG   0.005   0.001   ARG C 109 

*********************** 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
  175 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8414 (m-30) cc_final: 0.8115 (m-30)
REVERT: A  463 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6832 (ttt90)
REVERT: A  505 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7823 (mptt)
REVERT: A  560 TYR cc_start: 0.7942 (t80) cc_final: 0.7742 (t80)
REVERT: A  589 LYS cc_start: 0.8289 (tttp) cc_final: 0.8004 (ttpt)
REVERT: D    9 VAL cc_start: 0.8814 (t) cc_final: 0.8478 (p)
REVERT: B   21 MET cc_start: 0.8848 (ttp) cc_final: 0.8588 (ttt)
REVERT: B   88 LEU cc_start: 0.7906 (mp) cc_final: 0.7466 (tt)
REVERT: B   99 ASP cc_start: 0.8336 (m-30) cc_final: 0.8048 (m-30)
REVERT: B  142 ILE cc_start: 0.8423 (tp) cc_final: 0.8215 (pt)
REVERT: B  178 ASP cc_start: 0.7456 (m-30) cc_final: 0.7204 (m-30)
REVERT: B  463 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6775 (ttt90)
REVERT: B  472 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8732 (mmmm)
REVERT: B  499 MET cc_start: 0.8762 (ttp) cc_final: 0.8541 (ttm)
REVERT: B  505 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7844 (mptt)
REVERT: B  589 LYS cc_start: 0.8286 (tttp) cc_final: 0.7995 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2758
  time to fit residues: 62.1154
Evaluate side-chains
  128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:   30.0000
   chunk 38 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7936  Z= 0.195
  Angle     :  0.601   5.635  10790  Z= 0.326
  Chirality :  0.044   0.160   1246
  Planarity :  0.006   0.054   1326
  Dihedral  :  5.449  23.172   1084
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  8.31 %
    Favored  : 89.40 %
  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: -4.75 (0.21), residues: 976
  helix: -3.64 (0.14), residues: 530
  sheet: -1.98 (0.45), residues: 102
  loop : -2.28 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 144 
 HIS   0.005   0.001   HIS A   9 
 PHE   0.013   0.002   PHE D  72 
 TYR   0.016   0.001   TYR D  41 
 ARG   0.005   0.000   ARG D 109 

*********************** 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
  158 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8465 (m-30) cc_final: 0.7996 (m-30)
REVERT: A   11 MET cc_start: 0.8527 (mmt) cc_final: 0.8045 (mmt)
REVERT: A   88 LEU cc_start: 0.8005 (mp) cc_final: 0.7294 (tt)
REVERT: A   99 ASP cc_start: 0.8316 (m-30) cc_final: 0.8072 (m-30)
REVERT: A  463 ARG cc_start: 0.7000 (ttt180) cc_final: 0.6716 (mtp85)
REVERT: A  505 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7519 (mptt)
REVERT: A  539 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8452 (mpp80)
REVERT: A  589 LYS cc_start: 0.8427 (tttp) cc_final: 0.8113 (ttpt)
REVERT: C   38 MET cc_start: 0.7795 (mtt) cc_final: 0.7588 (mtp)
REVERT: D   38 MET cc_start: 0.7876 (mtt) cc_final: 0.7438 (mtm)
REVERT: B    6 ASP cc_start: 0.8474 (m-30) cc_final: 0.7936 (m-30)
REVERT: B   88 LEU cc_start: 0.7807 (mp) cc_final: 0.7546 (tt)
REVERT: B   99 ASP cc_start: 0.8281 (m-30) cc_final: 0.8045 (m-30)
REVERT: B  199 ASP cc_start: 0.7170 (p0) cc_final: 0.6408 (t0)
REVERT: B  463 ARG cc_start: 0.7015 (ttt180) cc_final: 0.6755 (mtp85)
REVERT: B  472 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8465 (mmmm)
REVERT: B  499 MET cc_start: 0.8678 (ttp) cc_final: 0.8360 (ttm)
REVERT: B  505 LYS cc_start: 0.7669 (mmtp) cc_final: 0.7367 (mptt)
REVERT: B  589 LYS cc_start: 0.8434 (tttp) cc_final: 0.8097 (ttpt)
  outliers start: 19
  outliers final: 10
  residues processed: 155
  average time/residue: 0.2111
  time to fit residues: 43.7076
Evaluate side-chains
  138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 CYS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   39 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0870
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.3958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7936  Z= 0.141
  Angle     :  0.525   5.303  10790  Z= 0.281
  Chirality :  0.042   0.146   1246
  Planarity :  0.005   0.047   1326
  Dihedral  :  4.871  23.236   1084
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.84 %
    Favored  : 86.63 %
  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: -3.69 (0.23), residues: 976
  helix: -2.65 (0.18), residues: 530
  sheet: -1.27 (0.47), residues: 102
  loop : -2.13 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.015   0.001   PHE B  87 
 TYR   0.015   0.001   TYR D  41 
 ARG   0.006   0.000   ARG D 109 

*********************** 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
  163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8488 (m-30) cc_final: 0.8010 (m-30)
REVERT: A   88 LEU cc_start: 0.7918 (mp) cc_final: 0.7322 (tt)
REVERT: A   92 LEU cc_start: 0.7485 (mp) cc_final: 0.7111 (tt)
REVERT: A   99 ASP cc_start: 0.8163 (m-30) cc_final: 0.7929 (m-30)
REVERT: A  180 ASP cc_start: 0.8015 (m-30) cc_final: 0.7462 (t0)
REVERT: A  539 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8331 (mpp80)
REVERT: A  589 LYS cc_start: 0.8375 (tttp) cc_final: 0.8065 (ttpt)
REVERT: C   38 MET cc_start: 0.7634 (mtt) cc_final: 0.7338 (mtm)
REVERT: D   38 MET cc_start: 0.7817 (mtt) cc_final: 0.7334 (mtm)
REVERT: B    6 ASP cc_start: 0.8489 (m-30) cc_final: 0.7931 (m-30)
REVERT: B   88 LEU cc_start: 0.7723 (mp) cc_final: 0.7511 (tt)
REVERT: B   99 ASP cc_start: 0.8083 (m-30) cc_final: 0.7850 (m-30)
REVERT: B  199 ASP cc_start: 0.7126 (p0) cc_final: 0.6400 (t0)
REVERT: B  499 MET cc_start: 0.8771 (ttp) cc_final: 0.8458 (ttm)
REVERT: B  589 LYS cc_start: 0.8416 (tttp) cc_final: 0.8121 (ttpt)
  outliers start: 21
  outliers final: 11
  residues processed: 159
  average time/residue: 0.2001
  time to fit residues: 42.6756
Evaluate side-chains
  138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 87 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 580 GLN
B 580 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7936  Z= 0.184
  Angle     :  0.532   5.305  10790  Z= 0.281
  Chirality :  0.043   0.158   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.622  21.546   1084
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.05 %
    Favored  : 84.58 %
  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: -3.10 (0.25), residues: 976
  helix: -2.17 (0.20), residues: 526
  sheet: -0.83 (0.49), residues: 102
  loop : -1.93 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 144 
 HIS   0.004   0.001   HIS B   9 
 PHE   0.009   0.001   PHE B  87 
 TYR   0.015   0.001   TYR C  41 
 ARG   0.005   0.000   ARG C 109 

*********************** 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
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8541 (m-30) cc_final: 0.8023 (m-30)
REVERT: A   18 TYR cc_start: 0.8609 (m-80) cc_final: 0.8297 (m-80)
REVERT: A   88 LEU cc_start: 0.7916 (mp) cc_final: 0.7381 (tt)
REVERT: A   99 ASP cc_start: 0.8173 (m-30) cc_final: 0.7953 (m-30)
REVERT: A  539 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8329 (mpp80)
REVERT: A  589 LYS cc_start: 0.8446 (tttp) cc_final: 0.8099 (ttpt)
REVERT: D   38 MET cc_start: 0.7742 (mtt) cc_final: 0.7217 (mtm)
REVERT: D   87 MET cc_start: 0.6265 (pmm) cc_final: 0.5362 (ppp)
REVERT: B    6 ASP cc_start: 0.8514 (m-30) cc_final: 0.8063 (m-30)
REVERT: B   11 MET cc_start: 0.8515 (mmt) cc_final: 0.8070 (mmt)
REVERT: B   92 LEU cc_start: 0.7320 (mp) cc_final: 0.6953 (tt)
REVERT: B   99 ASP cc_start: 0.8110 (m-30) cc_final: 0.7894 (m-30)
REVERT: B  199 ASP cc_start: 0.7126 (p0) cc_final: 0.6409 (t0)
REVERT: B  499 MET cc_start: 0.8844 (ttp) cc_final: 0.8527 (ttm)
REVERT: B  589 LYS cc_start: 0.8427 (tttp) cc_final: 0.8081 (ttpt)
  outliers start: 28
  outliers final: 18
  residues processed: 146
  average time/residue: 0.2163
  time to fit residues: 43.7716
Evaluate side-chains
  145 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 GLN
Chi-restraints excluded: chain A residue  582 ILE
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0970
   chunk 38 optimal weight:   30.0000
   chunk 79 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7936  Z= 0.164
  Angle     :  0.517  10.261  10790  Z= 0.267
  Chirality :  0.043   0.151   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.479  21.236   1084
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.01 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.25), residues: 976
  helix: -1.77 (0.21), residues: 526
  sheet: -0.65 (0.49), residues: 102
  loop : -1.83 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.015   0.001   PHE B  87 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.004   0.000   ARG C 109 

*********************** 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
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8646 (m-30) cc_final: 0.8142 (m-30)
REVERT: A   18 TYR cc_start: 0.8591 (m-80) cc_final: 0.8331 (m-80)
REVERT: A   88 LEU cc_start: 0.7919 (mp) cc_final: 0.7368 (tt)
REVERT: A   99 ASP cc_start: 0.8159 (m-30) cc_final: 0.7942 (m-30)
REVERT: A  531 ARG cc_start: 0.7795 (tpt170) cc_final: 0.7205 (ttm110)
REVERT: A  539 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8260 (mpp80)
REVERT: A  589 LYS cc_start: 0.8447 (tttp) cc_final: 0.8086 (ttpt)
REVERT: D   38 MET cc_start: 0.7649 (mtt) cc_final: 0.7128 (mtm)
REVERT: D   87 MET cc_start: 0.6300 (pmm) cc_final: 0.5402 (ppp)
REVERT: B    6 ASP cc_start: 0.8590 (m-30) cc_final: 0.8150 (m-30)
REVERT: B   99 ASP cc_start: 0.8104 (m-30) cc_final: 0.7896 (m-30)
REVERT: B  182 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6156 (tmm)
REVERT: B  499 MET cc_start: 0.8847 (ttp) cc_final: 0.8505 (ttm)
REVERT: B  589 LYS cc_start: 0.8441 (tttp) cc_final: 0.8083 (ttpt)
  outliers start: 22
  outliers final: 14
  residues processed: 150
  average time/residue: 0.1984
  time to fit residues: 40.4400
Evaluate side-chains
  140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0470
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 43 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7936  Z= 0.144
  Angle     :  0.488   8.389  10790  Z= 0.254
  Chirality :  0.042   0.143   1246
  Planarity :  0.005   0.049   1326
  Dihedral  :  4.301  20.055   1084
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.86 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.26), residues: 976
  helix: -1.32 (0.21), residues: 528
  sheet: -1.39 (0.46), residues: 126
  loop : -1.60 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 144 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.011   0.001   PHE B  87 
 TYR   0.013   0.001   TYR D  41 
 ARG   0.004   0.000   ARG C 109 

*********************** 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
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8650 (m-30) cc_final: 0.8223 (m-30)
REVERT: A   18 TYR cc_start: 0.8587 (m-80) cc_final: 0.8342 (m-80)
REVERT: A   88 LEU cc_start: 0.7866 (mp) cc_final: 0.7411 (tt)
REVERT: A  162 SER cc_start: 0.8383 (p) cc_final: 0.8176 (p)
REVERT: A  180 ASP cc_start: 0.8069 (m-30) cc_final: 0.7380 (t0)
REVERT: A  531 ARG cc_start: 0.7748 (tpt170) cc_final: 0.7118 (ttm110)
REVERT: A  539 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8270 (mpp80)
REVERT: A  589 LYS cc_start: 0.8416 (tttp) cc_final: 0.8087 (ttpt)
REVERT: D   38 MET cc_start: 0.7536 (mtt) cc_final: 0.7045 (mtm)
REVERT: D   87 MET cc_start: 0.6329 (pmm) cc_final: 0.5418 (ppp)
REVERT: B    6 ASP cc_start: 0.8633 (m-30) cc_final: 0.8201 (m-30)
REVERT: B   99 ASP cc_start: 0.8115 (m-30) cc_final: 0.7907 (m-30)
REVERT: B  499 MET cc_start: 0.8788 (ttp) cc_final: 0.8479 (ttm)
REVERT: B  575 GLN cc_start: 0.8710 (pp30) cc_final: 0.8345 (pp30)
REVERT: B  589 LYS cc_start: 0.8415 (tttp) cc_final: 0.8086 (ttpt)
  outliers start: 22
  outliers final: 16
  residues processed: 144
  average time/residue: 0.1959
  time to fit residues: 38.2455
Evaluate side-chains
  139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0170
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 36 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.8220

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

Flipped N/Q/H residues before XYZ refinement:
A 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7936  Z= 0.189
  Angle     :  0.505   7.418  10790  Z= 0.261
  Chirality :  0.043   0.140   1246
  Planarity :  0.005   0.046   1326
  Dihedral  :  4.329  19.093   1084
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.34 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.26), residues: 976
  helix: -1.17 (0.21), residues: 530
  sheet: -1.43 (0.44), residues: 136
  loop : -1.59 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  40 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.010   0.001   PHE B  87 
 TYR   0.016   0.001   TYR B 617 
 ARG   0.003   0.000   ARG C 109 

*********************** 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
  149 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8673 (m-30) cc_final: 0.8196 (m-30)
REVERT: A   88 LEU cc_start: 0.7875 (mp) cc_final: 0.7453 (tt)
REVERT: A  182 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6352 (tmm)
REVERT: A  184 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4316 (pp)
REVERT: A  539 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8234 (mpp80)
REVERT: A  589 LYS cc_start: 0.8390 (tttp) cc_final: 0.8064 (ttpt)
REVERT: D   87 MET cc_start: 0.6264 (pmm) cc_final: 0.5368 (ppp)
REVERT: B    6 ASP cc_start: 0.8642 (m-30) cc_final: 0.8242 (m-30)
REVERT: B  499 MET cc_start: 0.8807 (ttp) cc_final: 0.8510 (ttm)
REVERT: B  589 LYS cc_start: 0.8388 (tttp) cc_final: 0.8062 (ttpt)
  outliers start: 27
  outliers final: 20
  residues processed: 141
  average time/residue: 0.1970
  time to fit residues: 37.8651
Evaluate side-chains
  139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 GLN
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    0.1980
   chunk 17 optimal weight:    0.0980
   chunk 58 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7936  Z= 0.178
  Angle     :  0.500   6.899  10790  Z= 0.258
  Chirality :  0.043   0.135   1246
  Planarity :  0.005   0.044   1326
  Dihedral  :  4.305  18.715   1084
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.30 %
    Favored  : 82.29 %
  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: -1.94 (0.26), residues: 976
  helix: -0.92 (0.22), residues: 530
  sheet: -1.16 (0.45), residues: 126
  loop : -1.69 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 144 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.017   0.001   PHE B  87 
 TYR   0.018   0.001   TYR A 617 
 ARG   0.003   0.000   ARG C 109 

*********************** 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
  140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8652 (m-30) cc_final: 0.8224 (m-30)
REVERT: A   88 LEU cc_start: 0.7879 (mp) cc_final: 0.7503 (tt)
REVERT: A  539 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8166 (mpp80)
REVERT: A  589 LYS cc_start: 0.8400 (tttp) cc_final: 0.8062 (ttpt)
REVERT: D   25 SER cc_start: 0.6510 (m) cc_final: 0.6195 (t)
REVERT: D   87 MET cc_start: 0.6100 (pmm) cc_final: 0.5200 (ppp)
REVERT: B    6 ASP cc_start: 0.8682 (m-30) cc_final: 0.8279 (m-30)
REVERT: B  182 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5998 (tmm)
REVERT: B  472 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8306 (tptt)
REVERT: B  499 MET cc_start: 0.8807 (ttp) cc_final: 0.8503 (ttm)
REVERT: B  589 LYS cc_start: 0.8369 (tttp) cc_final: 0.8037 (ttpt)
  outliers start: 20
  outliers final: 17
  residues processed: 135
  average time/residue: 0.2084
  time to fit residues: 37.6949
Evaluate side-chains
  134 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 88 optimal weight:    0.1980
   chunk 51 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7936  Z= 0.175
  Angle     :  0.500   6.748  10790  Z= 0.258
  Chirality :  0.043   0.137   1246
  Planarity :  0.005   0.044   1326
  Dihedral  :  4.261  17.631   1084
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.30 %
    Favored  : 82.05 %
  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: -1.79 (0.26), residues: 976
  helix: -0.74 (0.22), residues: 532
  sheet: -1.13 (0.45), residues: 126
  loop : -1.73 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  37 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.017   0.001   PHE B  87 
 TYR   0.014   0.001   TYR B 560 
 ARG   0.008   0.000   ARG D 109 

*********************** 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
  142 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8698 (m-30) cc_final: 0.8276 (m-30)
REVERT: A   88 LEU cc_start: 0.7822 (mp) cc_final: 0.7452 (tt)
REVERT: A  163 GLU cc_start: 0.8219 (tp30) cc_final: 0.7998 (tp30)
REVERT: A  182 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6431 (tmm)
REVERT: A  539 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8118 (mpp80)
REVERT: A  589 LYS cc_start: 0.8319 (tttp) cc_final: 0.8019 (ttpt)
REVERT: D   25 SER cc_start: 0.6650 (m) cc_final: 0.6376 (t)
REVERT: D   87 MET cc_start: 0.6152 (pmm) cc_final: 0.5212 (ppp)
REVERT: B    6 ASP cc_start: 0.8686 (m-30) cc_final: 0.8270 (m-30)
REVERT: B   92 LEU cc_start: 0.7039 (mp) cc_final: 0.6807 (tt)
REVERT: B  182 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6118 (tmm)
REVERT: B  472 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8292 (tptt)
REVERT: B  499 MET cc_start: 0.8811 (ttp) cc_final: 0.8511 (ttm)
REVERT: B  589 LYS cc_start: 0.8318 (tttp) cc_final: 0.8013 (ttpt)
  outliers start: 22
  outliers final: 17
  residues processed: 135
  average time/residue: 0.2189
  time to fit residues: 40.2491
Evaluate side-chains
  137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 63 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0870
   chunk 76 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0040
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4972

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

Flipped N/Q/H residues before XYZ refinement:
A 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7936  Z= 0.137
  Angle     :  0.477   6.080  10790  Z= 0.246
  Chirality :  0.042   0.135   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.158  18.291   1084
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.18 %
    Favored  : 82.65 %
  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: -1.32 (0.26), residues: 976
  helix: -0.43 (0.22), residues: 534
  sheet: -0.25 (0.52), residues: 102
  loop : -1.62 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 144 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.019   0.001   PHE B  87 
 TYR   0.020   0.001   TYR B 617 
 ARG   0.008   0.000   ARG D 109 

********************** 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
  138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8663 (m-30) cc_final: 0.8294 (m-30)
REVERT: A   18 TYR cc_start: 0.8551 (m-80) cc_final: 0.8298 (m-80)
REVERT: A   88 LEU cc_start: 0.7754 (mp) cc_final: 0.7486 (tt)
REVERT: A   91 LYS cc_start: 0.8023 (tppt) cc_final: 0.7773 (mmtm)
REVERT: A  163 GLU cc_start: 0.8109 (tp30) cc_final: 0.7889 (tp30)
REVERT: A  182 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6464 (tmm)
REVERT: A  539 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8095 (mpp80)
REVERT: A  589 LYS cc_start: 0.8317 (tttp) cc_final: 0.8010 (ttpt)
REVERT: D   25 SER cc_start: 0.6608 (m) cc_final: 0.6350 (t)
REVERT: D   87 MET cc_start: 0.6084 (pmm) cc_final: 0.5178 (ppp)
REVERT: B    6 ASP cc_start: 0.8649 (m-30) cc_final: 0.8317 (m-30)
REVERT: B   92 LEU cc_start: 0.7035 (mp) cc_final: 0.6817 (tt)
REVERT: B  162 SER cc_start: 0.8193 (p) cc_final: 0.7981 (p)
REVERT: B  472 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8379 (tptt)
REVERT: B  589 LYS cc_start: 0.8318 (tttp) cc_final: 0.8011 (ttpt)
  outliers start: 18
  outliers final: 14
  residues processed: 131
  average time/residue: 0.2086
  time to fit residues: 36.9792
Evaluate side-chains
  130 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 GLN
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  580 GLN
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.0670
   chunk 70 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0170
   chunk 21 optimal weight:    0.3980
   chunk 76 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0270
   chunk 14 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.1814

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 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 = 0.3892 r_free = 0.3892 target = 0.174563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.111414 restraints weight = 9017.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.00
r_work: 0.2924 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7936  Z= 0.107
  Angle     :  0.469   6.135  10790  Z= 0.242
  Chirality :  0.041   0.137   1246
  Planarity :  0.004   0.044   1326
  Dihedral  :  4.066  18.625   1084
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 16.02 %
    Favored  : 82.77 %
  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: -0.93 (0.27), residues: 976
  helix: -0.00 (0.23), residues: 528
  sheet: -0.20 (0.53), residues: 102
  loop : -1.58 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 144 
 HIS   0.003   0.001   HIS B 203 
 PHE   0.018   0.001   PHE B  87 
 TYR   0.017   0.001   TYR B 617 
 ARG   0.008   0.000   ARG D 109 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1943.41 seconds
wall clock time: 36 minutes 39.30 seconds (2199.30 seconds total)