Starting phenix.real_space_refine
on Mon Mar 11 08:38:45 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/03_2024/7y9u_33692_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/03_2024/7y9u_33692.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/03_2024/7y9u_33692.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/03_2024/7y9u_33692_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/03_2024/7y9u_33692_updated.pdb"
  }
  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
    Residue "A ARG   94": "NH1" <-> "NH2"
    Residue "A ARG  475": "NH1" <-> "NH2"
    Residue "C ARG   23": "NH1" <-> "NH2"
    Residue "C ARG   71": "NH1" <-> "NH2"
    Residue "C ARG   76": "NH1" <-> "NH2"
    Residue "C ARG  101": "NH1" <-> "NH2"
    Residue "C ARG  109": "NH1" <-> "NH2"
    Residue "D ARG   23": "NH1" <-> "NH2"
    Residue "D ARG   71": "NH1" <-> "NH2"
    Residue "D ARG   76": "NH1" <-> "NH2"
    Residue "D ARG  101": "NH1" <-> "NH2"
    Residue "D ARG  109": "NH1" <-> "NH2"
    Residue "B ARG   94": "NH1" <-> "NH2"
    Residue "B ARG  475": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7748
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "D"
      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: "B"
      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: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'E7O': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'E7O': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.51, per 1000 atoms: 0.58
  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=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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.3 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...
  running ksdssp...
    Secondary structure from input PDB file:
      40 helices and 12 sheets defined
      44.3% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 29
      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 40 through 48
      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 51 through 59
      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 71 through 85
      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)
      removed outlier: 3.719A  pdb=" N   GLN A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LYS A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 90
      No H-bonds generated for 'chain 'A' and resid 87 through 90'
    Processing helix  chain 'A' and resid 99 through 109
      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)
    Processing helix  chain 'A' and resid 117 through 125
    Processing helix  chain 'A' and resid 129 through 142
      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 147 through 164
      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 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 458 through 473
      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)
    Processing helix  chain 'A' and resid 477 through 479
      No H-bonds generated for 'chain 'A' and resid 477 through 479'
    Processing helix  chain 'A' and resid 483 through 492
      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)
    Processing helix  chain 'A' and resid 501 through 507
    Processing helix  chain 'A' and resid 511 through 528
      removed outlier: 4.625A  pdb=" N   LEU A 515 " --> pdb=" O   ASP A 512 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLY A 516 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET A 517 " --> pdb=" O   GLY A 514 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ALA A 518 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   MET A 519 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 522 " --> pdb=" O   MET A 519 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU A 524 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE A 525 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET A 526 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 541
      No H-bonds generated for 'chain 'A' and resid 538 through 541'
    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 583 through 590
      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 597 through 607
      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)
    Processing helix  chain 'A' and resid 610 through 621
      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 4 through 29
      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 40 through 48
      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 51 through 59
      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 71 through 85
      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)
      removed outlier: 3.720A  pdb=" N   GLN B  78 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  76 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 90
      No H-bonds generated for 'chain 'B' and resid 87 through 90'
    Processing helix  chain 'B' and resid 99 through 109
      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)
    Processing helix  chain 'B' and resid 117 through 125
    Processing helix  chain 'B' and resid 129 through 142
      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 147 through 164
      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 169 through 171
      No H-bonds generated for 'chain 'B' and resid 169 through 171'
    Processing helix  chain 'B' and resid 458 through 473
      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)
    Processing helix  chain 'B' and resid 477 through 479
      No H-bonds generated for 'chain 'B' and resid 477 through 479'
    Processing helix  chain 'B' and resid 483 through 492
      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)
    Processing helix  chain 'B' and resid 501 through 507
    Processing helix  chain 'B' and resid 511 through 528
      removed outlier: 4.624A  pdb=" N   LEU B 515 " --> pdb=" O   ASP B 512 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLY B 516 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET B 517 " --> pdb=" O   GLY B 514 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ALA B 518 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET B 519 " --> pdb=" O   GLY B 516 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B 522 " --> pdb=" O   MET B 519 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU B 524 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE B 525 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET B 526 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 541
      No H-bonds generated for 'chain 'B' and resid 538 through 541'
    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 583 through 590
      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 597 through 607
      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)
    Processing helix  chain 'B' and resid 610 through 621
      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=  A, first strand: chain 'A' and resid 174 through 177
      removed outlier: 3.962A  pdb=" N   SER A 174 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
    Processing sheet with id=  B, 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=  C, 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=  D, 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=  E, first strand: chain 'C' and resid 97 through 100
      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: 4.267A  pdb=" N   TRP C  40 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA C  53 " --> pdb=" O   TRP C  40 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG C  42 " --> pdb=" O   TRP C  51 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   TRP C  51 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'C' and resid 101 through 103
    Processing sheet with id=  G, 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=  H, 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=  I, 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=  J, first strand: chain 'D' and resid 97 through 100
      removed outlier: 3.594A  pdb=" N   VAL D  97 " --> pdb=" O   GLN D  43 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   TRP D  40 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA D  53 " --> pdb=" O   TRP D  40 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG D  42 " --> pdb=" O   TRP D  51 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   TRP D  51 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'D' and resid 101 through 103
    Processing sheet with id=  L, first strand: chain 'B' and resid 174 through 177
      removed outlier: 3.961A  pdb=" N   SER B 174 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    585 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: 1.94

  Time building geometry restraints manager: 2.86 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:
       98.74 -   105.81: 198
      105.81 -   112.88: 4102
      112.88 -   119.95: 2998
      119.95 -   127.02: 3386
      127.02 -   134.09: 106
  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: 4416
       15.31 -    30.61: 190
       30.61 -    45.92: 54
       45.92 -    61.23: 6
       61.23 -    76.54: 2
  Dihedral angle restraints: 4668
    sinusoidal: 1806
      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 4665 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:
        2.31 -     2.83: 2396
        2.83 -     3.35: 6415
        3.35 -     3.86: 11798
        3.86 -     4.38: 13765
        4.38 -     4.90: 23897
  Nonbonded interactions: 58271
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 193 "
            pdb=" NE  ARG C 109 "
     model   vdw
     2.311 2.520
  nonbonded pdb=" OE2 GLU A 191 "
            pdb=" NH2 ARG C 101 "
     model   vdw
     2.340 2.520
  nonbonded pdb=" NH2 ARG C  71 "
            pdb=" O   SER C  89 "
     model   vdw
     2.352 2.520
  nonbonded pdb=" NH2 ARG D  71 "
            pdb=" O   SER D  89 "
     model   vdw
     2.352 2.520
  nonbonded pdb=" O   TRP A  89 "
            pdb=" OG  SER A  93 "
     model   vdw
     2.369 2.440
  ... (remaining 58266 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
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:             1.450
  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:          3.970
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     23.000
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.980
-------------------------------------------------------------------------------
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= 0.700
  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 : 2.311

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 fitting.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.829 
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: 0.2393
  time to fit residues: 53.5936
Evaluate side-chains
  128 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:   30.0000
   chunk 38 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0870
   chunk 45 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 112 ASN
B  43 ASN
B 112 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1964

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= 0.197
  Angle     :  0.568   5.510  10790  Z= 0.306
  Chirality :  0.043   0.154   1246
  Planarity :  0.006   0.053   1326
  Dihedral  :  5.365  24.311   1084
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  8.92 %
    Favored  : 88.43 %
  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: -4.77 (0.21), residues: 976
  helix: -3.76 (0.14), residues: 512
  sheet: -2.20 (0.44), residues: 92
  loop : -2.15 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  40 
 HIS   0.005   0.001   HIS A   9 
 PHE   0.012   0.002   PHE D  72 
 TYR   0.012   0.001   TYR D  41 
 ARG   0.005   0.000   ARG B 208 

*********************** 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
  161 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8469 (m-30) cc_final: 0.7984 (m-30)
REVERT: A   11 MET cc_start: 0.8506 (mmt) cc_final: 0.8058 (mmt)
REVERT: A   99 ASP cc_start: 0.8313 (m-30) cc_final: 0.8061 (m-30)
REVERT: A  162 SER cc_start: 0.8407 (p) cc_final: 0.8193 (p)
REVERT: A  463 ARG cc_start: 0.6913 (ttt180) cc_final: 0.6614 (mtp85)
REVERT: A  505 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7618 (mptt)
REVERT: A  539 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8496 (mpp80)
REVERT: A  589 LYS cc_start: 0.8322 (tttp) cc_final: 0.7977 (ttpt)
REVERT: D   38 MET cc_start: 0.7956 (mtt) cc_final: 0.7522 (mtm)
REVERT: B    6 ASP cc_start: 0.8503 (m-30) cc_final: 0.7965 (m-30)
REVERT: B   32 LYS cc_start: 0.8752 (mttp) cc_final: 0.8508 (mttm)
REVERT: B   88 LEU cc_start: 0.7783 (mp) cc_final: 0.7298 (tt)
REVERT: B   99 ASP cc_start: 0.8263 (m-30) cc_final: 0.8004 (m-30)
REVERT: B  499 MET cc_start: 0.8623 (ttp) cc_final: 0.8264 (ttm)
REVERT: B  505 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7625 (mptt)
REVERT: B  589 LYS cc_start: 0.8383 (tttp) cc_final: 0.8019 (ttpt)
  outliers start: 22
  outliers final: 10
  residues processed: 155
  average time/residue: 0.1971
  time to fit residues: 41.0837
Evaluate side-chains
  136 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 87 optimal weight:    0.3980
   chunk 94 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0040
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5992

-------------------------------------------------------------------------------
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: 0.8027
moved from start:          0.2399

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= 0.162
  Angle     :  0.514   5.291  10790  Z= 0.273
  Chirality :  0.042   0.143   1246
  Planarity :  0.005   0.047   1326
  Dihedral  :  4.789  24.099   1084
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 11.33 %
    Favored  : 85.42 %
  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: -4.02 (0.22), residues: 976
  helix: -3.05 (0.17), residues: 516
  sheet: -1.44 (0.46), residues: 104
  loop : -2.07 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  40 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.009   0.001   PHE D  72 
 TYR   0.011   0.001   TYR D  41 
 ARG   0.003   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
  158 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8510 (m-30) cc_final: 0.7980 (m-30)
REVERT: A   92 LEU cc_start: 0.7461 (mp) cc_final: 0.7085 (tt)
REVERT: A   99 ASP cc_start: 0.8148 (m-30) cc_final: 0.7925 (m-30)
REVERT: A  162 SER cc_start: 0.8394 (p) cc_final: 0.8161 (p)
REVERT: A  505 LYS cc_start: 0.7814 (mmtp) cc_final: 0.7590 (mptt)
REVERT: A  589 LYS cc_start: 0.8384 (tttp) cc_final: 0.7992 (ttpt)
REVERT: D   38 MET cc_start: 0.7877 (mtt) cc_final: 0.7343 (mtm)
REVERT: B    6 ASP cc_start: 0.8505 (m-30) cc_final: 0.7927 (m-30)
REVERT: B   75 ASP cc_start: 0.8140 (t70) cc_final: 0.7921 (t0)
REVERT: B   88 LEU cc_start: 0.7804 (mp) cc_final: 0.7289 (tt)
REVERT: B   99 ASP cc_start: 0.8101 (m-30) cc_final: 0.7878 (m-30)
REVERT: B  472 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8165 (tptt)
REVERT: B  499 MET cc_start: 0.8609 (ttp) cc_final: 0.8393 (ttm)
REVERT: B  505 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7574 (mptt)
REVERT: B  519 MET cc_start: 0.9056 (mmt) cc_final: 0.8849 (mmt)
REVERT: B  589 LYS cc_start: 0.8398 (tttp) cc_final: 0.8001 (ttpt)
  outliers start: 27
  outliers final: 16
  residues processed: 152
  average time/residue: 0.1998
  time to fit residues: 40.9129
Evaluate side-chains
  139 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
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  522 LEU
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   39 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  180 ASP
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  599 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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: 0.8050
moved from start:          0.2613

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= 0.212
  Angle     :  0.526   5.253  10790  Z= 0.278
  Chirality :  0.043   0.157   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.619  22.538   1084
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.01 %
    Favored  : 83.98 %
  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: -3.57 (0.24), residues: 976
  helix: -2.73 (0.19), residues: 522
  sheet: -0.89 (0.49), residues: 102
  loop : -1.89 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 144 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.008   0.001   PHE B 587 
 TYR   0.013   0.001   TYR B 560 
 ARG   0.002   0.000   ARG B  44 

*********************** 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
  152 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8593 (m-30) cc_final: 0.8020 (m-30)
REVERT: A   88 LEU cc_start: 0.8038 (mp) cc_final: 0.7254 (tt)
REVERT: A   92 LEU cc_start: 0.7433 (mp) cc_final: 0.6984 (tt)
REVERT: A   99 ASP cc_start: 0.8165 (m-30) cc_final: 0.7928 (m-30)
REVERT: A  162 SER cc_start: 0.8420 (p) cc_final: 0.8182 (p)
REVERT: A  472 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8408 (tptt)
REVERT: A  505 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7603 (mptt)
REVERT: A  589 LYS cc_start: 0.8419 (tttp) cc_final: 0.8000 (ttpt)
REVERT: D   38 MET cc_start: 0.7838 (mtt) cc_final: 0.7277 (mtm)
REVERT: D   87 MET cc_start: 0.6239 (pmm) cc_final: 0.5499 (ppp)
REVERT: B    6 ASP cc_start: 0.8529 (m-30) cc_final: 0.7982 (m-30)
REVERT: B   88 LEU cc_start: 0.7824 (mp) cc_final: 0.7339 (tt)
REVERT: B   99 ASP cc_start: 0.8113 (m-30) cc_final: 0.7883 (m-30)
REVERT: B  499 MET cc_start: 0.8667 (ttp) cc_final: 0.8427 (ttm)
REVERT: B  505 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7604 (mptt)
REVERT: B  519 MET cc_start: 0.9074 (mmt) cc_final: 0.8825 (mmt)
REVERT: B  589 LYS cc_start: 0.8423 (tttp) cc_final: 0.8006 (ttpt)
  outliers start: 25
  outliers final: 18
  residues processed: 147
  average time/residue: 0.2010
  time to fit residues: 39.9518
Evaluate side-chains
  139 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
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  522 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 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   39 CYS
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  180 ASP
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  599 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 1 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 83 optimal weight:    0.0070
   chunk 23 optimal weight:    0.0010
   chunk 31 optimal weight:    0.0030
   overall best weight:    0.2414

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0.7979
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7936  Z= 0.106
  Angle     :  0.464   5.581  10790  Z= 0.244
  Chirality :  0.040   0.147   1246
  Planarity :  0.004   0.045   1326
  Dihedral  :  4.182  21.947   1084
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.61 %
    Favored  : 83.98 %
  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: -2.83 (0.25), residues: 976
  helix: -2.10 (0.20), residues: 506
  sheet: -0.65 (0.50), residues: 102
  loop : -1.63 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  40 
 HIS   0.003   0.001   HIS B   9 
 PHE   0.005   0.001   PHE B   7 
 TYR   0.012   0.001   TYR B 560 
 ARG   0.005   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
  165 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8589 (m-30) cc_final: 0.8067 (m-30)
REVERT: A   11 MET cc_start: 0.8349 (mmt) cc_final: 0.7969 (mmt)
REVERT: A   88 LEU cc_start: 0.7974 (mp) cc_final: 0.7227 (tt)
REVERT: A   92 LEU cc_start: 0.7238 (mp) cc_final: 0.6937 (tt)
REVERT: A  472 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8494 (tptt)
REVERT: A  505 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7575 (mptt)
REVERT: A  589 LYS cc_start: 0.8356 (tttp) cc_final: 0.7943 (ttpt)
REVERT: D   38 MET cc_start: 0.7656 (mtt) cc_final: 0.7175 (mtm)
REVERT: B    6 ASP cc_start: 0.8570 (m-30) cc_final: 0.8186 (m-30)
REVERT: B   88 LEU cc_start: 0.7793 (mp) cc_final: 0.7275 (tt)
REVERT: B   92 LEU cc_start: 0.7351 (mp) cc_final: 0.7012 (tt)
REVERT: B  199 ASP cc_start: 0.7239 (p0) cc_final: 0.6427 (t0)
REVERT: B  499 MET cc_start: 0.8616 (ttp) cc_final: 0.8209 (ttm)
REVERT: B  505 LYS cc_start: 0.7783 (mmtp) cc_final: 0.7470 (mptt)
REVERT: B  589 LYS cc_start: 0.8382 (tttp) cc_final: 0.7966 (ttpt)
  outliers start: 20
  outliers final: 12
  residues processed: 160
  average time/residue: 0.1814
  time to fit residues: 39.7623
Evaluate side-chains
  137 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  557 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   97 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  599 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 89 optimal weight:    0.4980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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: 0.8037
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7936  Z= 0.207
  Angle     :  0.509   5.276  10790  Z= 0.264
  Chirality :  0.043   0.141   1246
  Planarity :  0.005   0.050   1326
  Dihedral  :  4.267  20.259   1084
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.73 %
    Favored  : 83.13 %
  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: -2.74 (0.24), residues: 976
  helix: -1.96 (0.20), residues: 512
  sheet: -0.49 (0.51), residues: 102
  loop : -1.71 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A 176 
 PHE   0.007   0.001   PHE A 493 
 TYR   0.011   0.001   TYR B 560 
 ARG   0.004   0.000   ARG D 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
  143 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8675 (m-30) cc_final: 0.8165 (m-30)
REVERT: A   92 LEU cc_start: 0.7220 (mp) cc_final: 0.6980 (tt)
REVERT: A  455 MET cc_start: 0.7136 (tpt) cc_final: 0.6906 (mmm)
REVERT: A  472 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8508 (tptt)
REVERT: A  505 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7543 (mptt)
REVERT: A  589 LYS cc_start: 0.8348 (tttp) cc_final: 0.7992 (ttpt)
REVERT: D   38 MET cc_start: 0.7665 (mtt) cc_final: 0.7465 (mtm)
REVERT: D   87 MET cc_start: 0.6088 (pmm) cc_final: 0.5325 (ppp)
REVERT: B    6 ASP cc_start: 0.8629 (m-30) cc_final: 0.8204 (m-30)
REVERT: B   88 LEU cc_start: 0.7777 (mp) cc_final: 0.7224 (tt)
REVERT: B   92 LEU cc_start: 0.7330 (mp) cc_final: 0.6920 (tt)
REVERT: B  184 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4480 (pp)
REVERT: B  455 MET cc_start: 0.7380 (tpt) cc_final: 0.7142 (mmm)
REVERT: B  499 MET cc_start: 0.8704 (ttp) cc_final: 0.8390 (ttm)
REVERT: B  505 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7458 (mptt)
REVERT: B  519 MET cc_start: 0.8991 (mmp) cc_final: 0.8745 (mmt)
REVERT: B  589 LYS cc_start: 0.8347 (tttp) cc_final: 0.7988 (ttpt)
  outliers start: 26
  outliers final: 19
  residues processed: 134
  average time/residue: 0.1957
  time to fit residues: 35.7892
Evaluate side-chains
  135 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  522 LEU
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  174 SER
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  555 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 56 optimal weight:   20.0000
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0.8066
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7936  Z= 0.281
  Angle     :  0.540   5.290  10790  Z= 0.279
  Chirality :  0.044   0.135   1246
  Planarity :  0.005   0.046   1326
  Dihedral  :  4.449  20.470   1084
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 13.01 %
    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: -2.72 (0.24), residues: 976
  helix: -1.94 (0.20), residues: 528
  sheet: -0.38 (0.52), residues: 102
  loop : -1.72 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A 594 
 PHE   0.010   0.002   PHE B 587 
 TYR   0.012   0.001   TYR D  99 
 ARG   0.003   0.000   ARG D 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
  160 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8704 (m-30) cc_final: 0.8173 (m-30)
REVERT: A   88 LEU cc_start: 0.7984 (mp) cc_final: 0.7225 (tt)
REVERT: A   92 LEU cc_start: 0.7347 (mp) cc_final: 0.6979 (tt)
REVERT: A  184 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4637 (pp)
REVERT: A  472 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8563 (tptt)
REVERT: A  505 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7552 (mmtm)
REVERT: A  589 LYS cc_start: 0.8334 (tttp) cc_final: 0.7972 (ttpt)
REVERT: C   25 SER cc_start: 0.7237 (m) cc_final: 0.6451 (t)
REVERT: D   87 MET cc_start: 0.5831 (pmm) cc_final: 0.5154 (ppp)
REVERT: B    6 ASP cc_start: 0.8694 (m-30) cc_final: 0.8200 (m-30)
REVERT: B   88 LEU cc_start: 0.7792 (mp) cc_final: 0.7196 (tt)
REVERT: B   92 LEU cc_start: 0.7355 (mp) cc_final: 0.6999 (tt)
REVERT: B  499 MET cc_start: 0.8715 (ttp) cc_final: 0.8389 (ttm)
REVERT: B  505 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7552 (mmtm)
REVERT: B  589 LYS cc_start: 0.8332 (tttp) cc_final: 0.7965 (ttpt)
  outliers start: 29
  outliers final: 19
  residues processed: 152
  average time/residue: 0.1982
  time to fit residues: 40.9411
Evaluate side-chains
  136 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  522 LEU
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  117 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  113 THR
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  555 MET
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0970
   chunk 88 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
C  86 GLN
** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7936  Z= 0.182
  Angle     :  0.497   6.322  10790  Z= 0.257
  Chirality :  0.042   0.136   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.273  19.619   1084
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.22 %
    Favored  : 83.01 %
  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: -2.26 (0.25), residues: 976
  helix: -1.52 (0.21), residues: 520
  sheet: -0.27 (0.52), residues: 102
  loop : -1.58 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  37 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.024   0.001   PHE B  87 
 TYR   0.009   0.001   TYR D  41 
 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
  144 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8683 (m-30) cc_final: 0.8260 (m-30)
REVERT: A   88 LEU cc_start: 0.7938 (mp) cc_final: 0.7198 (tt)
REVERT: A   92 LEU cc_start: 0.7316 (mp) cc_final: 0.6948 (tt)
REVERT: A  472 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8487 (tptt)
REVERT: A  505 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7635 (mmtm)
REVERT: A  589 LYS cc_start: 0.8278 (tttp) cc_final: 0.7927 (ttpt)
REVERT: D   87 MET cc_start: 0.5610 (pmm) cc_final: 0.4972 (ppp)
REVERT: B    6 ASP cc_start: 0.8666 (m-30) cc_final: 0.8217 (m-30)
REVERT: B   88 LEU cc_start: 0.7827 (mp) cc_final: 0.7204 (tt)
REVERT: B   92 LEU cc_start: 0.7297 (mp) cc_final: 0.6962 (tt)
REVERT: B  499 MET cc_start: 0.8703 (ttp) cc_final: 0.8356 (ttm)
REVERT: B  505 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7514 (mmtm)
REVERT: B  589 LYS cc_start: 0.8269 (tttp) cc_final: 0.7923 (ttpt)
  outliers start: 23
  outliers final: 22
  residues processed: 136
  average time/residue: 0.1941
  time to fit residues: 35.9098
Evaluate side-chains
  140 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain C residue   44 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   83 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 67 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0070
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0.8015
moved from start:          0.3371

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= 0.146
  Angle     :  0.479   6.462  10790  Z= 0.247
  Chirality :  0.041   0.137   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.087  18.536   1084
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.46 %
    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: -1.84 (0.26), residues: 976
  helix: -1.09 (0.22), residues: 518
  sheet: -0.15 (0.52), residues: 102
  loop : -1.51 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  37 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.019   0.001   PHE B  87 
 TYR   0.019   0.001   TYR B 617 
 ARG   0.003   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
  146 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8662 (m-30) cc_final: 0.8215 (m-30)
REVERT: A   88 LEU cc_start: 0.7950 (mp) cc_final: 0.7247 (tt)
REVERT: A   92 LEU cc_start: 0.7155 (mp) cc_final: 0.6930 (tt)
REVERT: A  162 SER cc_start: 0.8228 (p) cc_final: 0.8013 (p)
REVERT: A  472 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8474 (tptt)
REVERT: A  505 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7443 (mmtm)
REVERT: A  589 LYS cc_start: 0.8250 (tttp) cc_final: 0.7908 (ttpt)
REVERT: D   87 MET cc_start: 0.5672 (pmm) cc_final: 0.5025 (ppp)
REVERT: B    6 ASP cc_start: 0.8611 (m-30) cc_final: 0.8254 (m-30)
REVERT: B   88 LEU cc_start: 0.7814 (mp) cc_final: 0.7266 (tt)
REVERT: B   92 LEU cc_start: 0.7280 (mp) cc_final: 0.6949 (tt)
REVERT: B  499 MET cc_start: 0.8691 (ttp) cc_final: 0.8342 (ttm)
REVERT: B  589 LYS cc_start: 0.8270 (tttp) cc_final: 0.7906 (ttpt)
  outliers start: 23
  outliers final: 21
  residues processed: 141
  average time/residue: 0.2111
  time to fit residues: 40.3570
Evaluate side-chains
  141 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 THR
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  494 LYS
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain C residue   44 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   83 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  113 THR
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  557 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 88 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   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 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: 0.8030
moved from start:          0.3406

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= 0.179
  Angle     :  0.501   6.336  10790  Z= 0.255
  Chirality :  0.042   0.132   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.114  17.825   1084
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.58 %
    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: -1.74 (0.26), residues: 976
  helix: -0.97 (0.22), residues: 520
  sheet: -0.11 (0.53), residues: 102
  loop : -1.55 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.018   0.001   PHE B  87 
 TYR   0.018   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
  141 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8653 (m-30) cc_final: 0.8160 (m-30)
REVERT: A   88 LEU cc_start: 0.7928 (mp) cc_final: 0.7218 (tt)
REVERT: A   92 LEU cc_start: 0.7328 (mp) cc_final: 0.6989 (tt)
REVERT: A  162 SER cc_start: 0.8235 (p) cc_final: 0.8025 (p)
REVERT: A  472 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8529 (tptt)
REVERT: A  505 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7413 (mmtm)
REVERT: A  589 LYS cc_start: 0.8255 (tttp) cc_final: 0.7916 (ttpt)
REVERT: D   87 MET cc_start: 0.5620 (pmm) cc_final: 0.4992 (ppp)
REVERT: B    6 ASP cc_start: 0.8628 (m-30) cc_final: 0.8226 (m-30)
REVERT: B   92 LEU cc_start: 0.7314 (mp) cc_final: 0.6932 (tt)
REVERT: B  499 MET cc_start: 0.8707 (ttp) cc_final: 0.8369 (ttm)
REVERT: B  589 LYS cc_start: 0.8275 (tttp) cc_final: 0.7909 (ttpt)
  outliers start: 22
  outliers final: 21
  residues processed: 136
  average time/residue: 0.1914
  time to fit residues: 35.5326
Evaluate side-chains
  139 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  174 SER
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain C residue   44 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   83 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  526 MET
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0060
   chunk 76 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 66 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.168687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.110244 restraints weight = 9081.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.18
r_work: 0.2843 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3499

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= 0.147
  Angle     :  0.478   6.247  10790  Z= 0.244
  Chirality :  0.041   0.132   1246
  Planarity :  0.005   0.045   1326
  Dihedral  :  4.012  17.518   1084
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.18 %
    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: -1.50 (0.26), residues: 976
  helix: -0.73 (0.22), residues: 518
  sheet: -0.06 (0.53), residues: 102
  loop : -1.49 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  37 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.016   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: 1944.39 seconds
wall clock time: 35 minutes 48.09 seconds (2148.09 seconds total)