Starting phenix.real_space_refine
on Fri Feb 14 14:23:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6320      2.51       5
     N    1740      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10002
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 4963
          Classifications: {'peptide': 741}
          Incomplete info: {'truncation_to_alanine': 235}
          Link IDs: {'PTRANS': 28, 'TRANS': 712}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 953
          Unresolved non-hydrogen angles: 1211
          Unresolved non-hydrogen dihedrals: 815
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 9, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 588
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'CWY': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.97, per 1000 atoms: 1.00
  Number of scatterers: 10002
  At special positions: 0
  Unit cell: (104.442, 84.162, 179.478, 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      66     16.00
     O    1876      8.00
     N    1740      7.00
     C    6320      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 527 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 361 " - pdb=" SG  CYS A 373 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 412 " - pdb=" SG  CYS A 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 509 " - pdb=" SG  CYS A 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 513 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 546 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 549 " - pdb=" SG  CYS A 562 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 641 " - pdb=" SG  CYS A 730 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 209 "
      " NAG B 901 " - " ASN B 209 "
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2800

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 14 sheets defined
      34.8% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 78
      removed outlier: 4.559A  pdb=" N   ALA A  71 " --> pdb=" O   GLN A  67 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.508A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 106 " --> pdb=" O   ASP A 102 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLU A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   GLU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE A 112 " --> pdb=" O   GLN A 108 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 4.017A  pdb=" N   GLN A 156 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.721A  pdb=" N   SER A 179 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP A 180 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 176 through 180'
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 4.266A  pdb=" N   ALA A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 203 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 256 through 261
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 4.074A  pdb=" N   LYS A 266 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.719A  pdb=" N   LEU A 340 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 359
    Processing helix  chain 'A' and resid 387 through 389
      No H-bonds generated for 'chain 'A' and resid 387 through 389'
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.744A  pdb=" N   TYR A 398 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   MET A 400 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   HIS A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.546A  pdb=" N   CYS A 412 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 431
    Processing helix  chain 'A' and resid 499 through 503
      removed outlier: 3.518A  pdb=" N   ASN A 502 " --> pdb=" O   TRP A 499 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A 503 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 499 through 503'
    Processing helix  chain 'A' and resid 578 through 586
      removed outlier: 3.525A  pdb=" N   THR A 582 " --> pdb=" O   ILE A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.227A  pdb=" N   THR A 591 " --> pdb=" O   GLY A 587 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS A 592 " --> pdb=" O   PHE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 614 through 619
    Processing helix  chain 'A' and resid 619 through 626
    Processing helix  chain 'A' and resid 640 through 652
      removed outlier: 3.508A  pdb=" N   ARG A 645 " --> pdb=" O   CYS A 641 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 649 " --> pdb=" O   ARG A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 666
      removed outlier: 3.897A  pdb=" N   ASN A 664 " --> pdb=" O   LEU A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 696
    Processing helix  chain 'A' and resid 701 through 709
    Processing helix  chain 'A' and resid 733 through 750
      removed outlier: 3.922A  pdb=" N   ASP A 744 " --> pdb=" O   SER A 740 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 746 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LEU A 747 " --> pdb=" O   TYR A 743 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 750 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 755
    Processing helix  chain 'A' and resid 766 through 783
      removed outlier: 4.886A  pdb=" N   GLY A 772 " --> pdb=" O   ALA A 768 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   PHE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 778 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   CYS A 779 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE A 781 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP A 782 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 789
    Processing helix  chain 'A' and resid 799 through 813
      removed outlier: 3.681A  pdb=" N   MET A 803 " --> pdb=" O   GLN A 799 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS A 804 " --> pdb=" O   THR A 800 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 807 " --> pdb=" O   MET A 803 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A 808 " --> pdb=" O   CYS A 804 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A 809 " --> pdb=" O   ILE A 805 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   SER A 810 " --> pdb=" O   SER A 806 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 78
      removed outlier: 4.560A  pdb=" N   ALA B  71 " --> pdb=" O   GLN B  67 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.508A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU B 107 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   GLU B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE B 112 " --> pdb=" O   GLN B 108 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 156
      removed outlier: 4.017A  pdb=" N   GLN B 156 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
      removed outlier: 3.720A  pdb=" N   SER B 179 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP B 180 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 176 through 180'
    Processing helix  chain 'B' and resid 194 through 203
      removed outlier: 4.266A  pdb=" N   ALA B 200 " --> pdb=" O   TYR B 196 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU B 203 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
    Processing helix  chain 'B' and resid 256 through 261
    Processing helix  chain 'B' and resid 261 through 266
      removed outlier: 4.075A  pdb=" N   LYS B 266 " --> pdb=" O   GLU B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 340
      removed outlier: 3.720A  pdb=" N   LEU B 340 " --> pdb=" O   PHE B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 359
    Processing helix  chain 'B' and resid 387 through 389
      No H-bonds generated for 'chain 'B' and resid 387 through 389'
    Processing helix  chain 'B' and resid 390 through 407
      removed outlier: 3.744A  pdb=" N   TYR B 398 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   MET B 400 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS B 405 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 412
      removed outlier: 3.546A  pdb=" N   CYS B 412 " --> pdb=" O   GLN B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 431
    Processing helix  chain 'B' and resid 499 through 503
      removed outlier: 3.518A  pdb=" N   ASN B 502 " --> pdb=" O   TRP B 499 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B 503 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 499 through 503'
    Processing helix  chain 'B' and resid 578 through 586
      removed outlier: 3.524A  pdb=" N   THR B 582 " --> pdb=" O   ILE B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 594
      removed outlier: 4.226A  pdb=" N   THR B 591 " --> pdb=" O   GLY B 587 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS B 592 " --> pdb=" O   PHE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 599
    Processing helix  chain 'B' and resid 604 through 609
    Processing helix  chain 'B' and resid 614 through 619
    Processing helix  chain 'B' and resid 619 through 626
    Processing helix  chain 'B' and resid 640 through 652
      removed outlier: 3.508A  pdb=" N   ARG B 645 " --> pdb=" O   CYS B 641 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY B 649 " --> pdb=" O   ARG B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 3.896A  pdb=" N   ASN B 664 " --> pdb=" O   LEU B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 696
    Processing helix  chain 'B' and resid 701 through 709
    Processing helix  chain 'B' and resid 733 through 750
      removed outlier: 3.922A  pdb=" N   ASP B 744 " --> pdb=" O   SER B 740 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE B 746 " --> pdb=" O   THR B 742 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LEU B 747 " --> pdb=" O   TYR B 743 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 750 " --> pdb=" O   ILE B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 755
    Processing helix  chain 'B' and resid 766 through 783
      removed outlier: 4.887A  pdb=" N   GLY B 772 " --> pdb=" O   ALA B 768 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   PHE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR B 778 " --> pdb=" O   THR B 774 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   CYS B 779 " --> pdb=" O   MET B 775 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE B 781 " --> pdb=" O   THR B 777 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP B 782 " --> pdb=" O   THR B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 789
    Processing helix  chain 'B' and resid 799 through 813
      removed outlier: 3.683A  pdb=" N   MET B 803 " --> pdb=" O   GLN B 799 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS B 804 " --> pdb=" O   THR B 800 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL B 807 " --> pdb=" O   MET B 803 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER B 808 " --> pdb=" O   CYS B 804 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU B 809 " --> pdb=" O   ILE B 805 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER B 810 " --> pdb=" O   SER B 806 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS A 240 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR A 215 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU A 245 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS A 240 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR A 215 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   VAL A 271 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 272 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TRP A 297 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 469 through 470
    Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 555
    Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 34
    Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 34
    Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS B 240 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR B 215 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU B 245 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS B 240 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR B 215 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   VAL B 271 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL B 272 " --> pdb=" O   THR B 296 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TRP B 297 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 469 through 470
    Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 539
    Processing sheet with id=AB5, first strand: chain 'B' and resid 553 through 555

    238 hydrogen bonds defined for protein.
    672 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: 3.29

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1700
        1.31 -     1.44: 2573
        1.44 -     1.57: 5821
        1.57 -     1.70: 4
        1.70 -     1.83: 82
  Bond restraints: 10180
  Sorted by residual:
  bond pdb=" C   CWY A 902 "
       pdb=" C7  CWY A 902 "
    ideal  model  delta    sigma   weight residual
    1.537  1.315  0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" C   CWY B 902 "
       pdb=" C7  CWY B 902 "
    ideal  model  delta    sigma   weight residual
    1.537  1.316  0.221 2.00e-02 2.50e+03 1.22e+02
  bond pdb=" C1  CWY A 902 "
       pdb=" C3  CWY A 902 "
    ideal  model  delta    sigma   weight residual
    1.533  1.355  0.178 2.00e-02 2.50e+03 7.94e+01
  bond pdb=" C1  CWY B 902 "
       pdb=" C3  CWY B 902 "
    ideal  model  delta    sigma   weight residual
    1.533  1.355  0.178 2.00e-02 2.50e+03 7.92e+01
  bond pdb=" C8  CWY A 902 "
       pdb=" N1  CWY A 902 "
    ideal  model  delta    sigma   weight residual
    1.342  1.461 -0.119 2.00e-02 2.50e+03 3.53e+01
  ... (remaining 10175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.66: 13910
        5.66 -    11.31: 50
       11.31 -    16.97: 6
       16.97 -    22.63: 0
       22.63 -    28.28: 2
  Bond angle restraints: 13968
  Sorted by residual:
  angle pdb=" C4  CWY A 902 "
        pdb=" C6  CWY A 902 "
        pdb=" C7  CWY A 902 "
      ideal   model   delta    sigma   weight residual
     116.66  144.94  -28.28 3.00e+00 1.11e-01 8.89e+01
  angle pdb=" C4  CWY B 902 "
        pdb=" C6  CWY B 902 "
        pdb=" C7  CWY B 902 "
      ideal   model   delta    sigma   weight residual
     116.66  144.92  -28.26 3.00e+00 1.11e-01 8.87e+01
  angle pdb=" C   TRP B 486 "
        pdb=" N   ALA B 487 "
        pdb=" CA  ALA B 487 "
      ideal   model   delta    sigma   weight residual
     121.54  133.51  -11.97 1.91e+00 2.74e-01 3.93e+01
  angle pdb=" C   TRP A 486 "
        pdb=" N   ALA A 487 "
        pdb=" CA  ALA A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  133.49  -11.95 1.91e+00 2.74e-01 3.92e+01
  angle pdb=" C   VAL A 247 "
        pdb=" CA  VAL A 247 "
        pdb=" CB  VAL A 247 "
      ideal   model   delta    sigma   weight residual
     110.70  116.28   -5.58 9.90e-01 1.02e+00 3.18e+01
  ... (remaining 13963 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 5540
       17.78 -    35.57: 450
       35.57 -    53.35: 81
       53.35 -    71.13: 26
       71.13 -    88.91: 11
  Dihedral angle restraints: 6108
    sinusoidal: 1800
      harmonic: 4308
  Sorted by residual:
  dihedral pdb=" CB  CYS A 240 "
           pdb=" SG  CYS A 240 "
           pdb=" SG  CYS A 527 "
           pdb=" CB  CYS A 527 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.62  -82.38     1      1.00e+01 1.00e-02 8.33e+01
  dihedral pdb=" CB  CYS A 361 "
           pdb=" SG  CYS A 361 "
           pdb=" SG  CYS A 373 "
           pdb=" CB  CYS A 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.16   57.16     1      1.00e+01 1.00e-02 4.39e+01
  dihedral pdb=" CA  ALA B 487 "
           pdb=" C   ALA B 487 "
           pdb=" N   GLU B 488 "
           pdb=" CA  GLU B 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.10   30.90     0      5.00e+00 4.00e-02 3.82e+01
  ... (remaining 6105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.165: 1698
       0.165 -    0.329: 8
       0.329 -    0.494: 2
       0.494 -    0.659: 2
       0.659 -    0.823: 2
  Chirality restraints: 1712
  Sorted by residual:
  chirality pdb=" C6  CWY A 902 "
            pdb=" C3  CWY A 902 "
            pdb=" C4  CWY A 902 "
            pdb=" C7  CWY A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.64    1.81    0.82 2.00e-01 2.50e+01 1.70e+01
  chirality pdb=" C6  CWY B 902 "
            pdb=" C3  CWY B 902 "
            pdb=" C4  CWY B 902 "
            pdb=" C7  CWY B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.64    1.82    0.82 2.00e-01 2.50e+01 1.69e+01
  chirality pdb=" C3  CWY A 902 "
            pdb=" C1  CWY A 902 "
            pdb=" C4  CWY A 902 "
            pdb=" C6  CWY A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.61    2.03    0.58 2.00e-01 2.50e+01 8.33e+00
  ... (remaining 1709 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 247 "    0.017 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   VAL B 247 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   VAL B 247 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLY B 248 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 247 "   -0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   VAL A 247 "    0.060 2.00e-02 2.50e+03
        pdb=" O   VAL A 247 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLY A 248 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 637 "    0.041 5.00e-02 4.00e+02   6.23e-02 6.20e+00
        pdb=" N   PRO B 638 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 638 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 638 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 106
        2.60 -     3.17: 7824
        3.17 -     3.75: 14827
        3.75 -     4.32: 19164
        4.32 -     4.90: 30741
  Nonbonded interactions: 72662
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 361 "
            pdb=" SG  CYS B 373 "
     model   vdw
     2.024 3.760
  nonbonded pdb=" SG  CYS B 412 "
            pdb=" SG  CYS B 419 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 509 "
            pdb=" SG  CYS B 528 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 549 "
            pdb=" SG  CYS B 562 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS B 513 "
            pdb=" SG  CYS B 531 "
     model   vdw
     2.033 3.760
  ... (remaining 72657 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     29.230
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.050
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.222  10180  Z= 0.469
  Angle     :  1.033  28.282  13968  Z= 0.544
  Chirality :  0.064   0.823   1712
  Planarity :  0.006   0.062   1826
  Dihedral  : 14.904  88.913   3284
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 10.81 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.56 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -6.08 (0.15), residues: 1462
  helix: -4.83 (0.07), residues: 508
  sheet: -4.23 (0.29), residues: 164
  loop : -3.46 (0.18), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 486 
 HIS   0.006   0.001   HIS B  94 
 PHE   0.015   0.001   PHE B  45 
 TYR   0.012   0.001   TYR B 539 
 ARG   0.002   0.000   ARG A 253 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  630 PHE cc_start: 0.8383 (m-10) cc_final: 0.7977 (m-80)
REVERT: B  630 PHE cc_start: 0.8335 (m-10) cc_final: 0.7912 (m-80)
  outliers start: 6
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1974
  time to fit residues: 41.6273
Evaluate side-chains
  105 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 134 optimal weight:   10.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
A 467 ASN
B  80 ASN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 238 ASN
B 467 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.217260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.163422 restraints weight = 14283.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.159813 restraints weight = 14016.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.162042 restraints weight = 11057.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10180  Z= 0.279
  Angle     :  0.693   9.649  13968  Z= 0.369
  Chirality :  0.044   0.142   1712
  Planarity :  0.005   0.052   1826
  Dihedral  :  9.650  84.093   1654
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.01 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.29 %
    Favored  : 84.15 %
  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: -5.36 (0.17), residues: 1462
  helix: -3.97 (0.13), residues: 524
  sheet: -3.70 (0.34), residues: 168
  loop : -3.24 (0.20), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 297 
 HIS   0.003   0.001   HIS A 485 
 PHE   0.014   0.001   PHE B 471 
 TYR   0.010   0.002   TYR A 466 
 ARG   0.002   0.000   ARG A 183 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 ASP cc_start: 0.8101 (m-30) cc_final: 0.7862 (m-30)
REVERT: A  204 ILE cc_start: 0.8941 (tp) cc_final: 0.8641 (tp)
REVERT: A  630 PHE cc_start: 0.8039 (m-10) cc_final: 0.7789 (m-80)
REVERT: B  194 ASP cc_start: 0.8093 (m-30) cc_final: 0.7877 (m-30)
REVERT: B  204 ILE cc_start: 0.8895 (tp) cc_final: 0.8577 (tp)
REVERT: B  630 PHE cc_start: 0.7983 (m-10) cc_final: 0.7714 (m-80)
  outliers start: 21
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1832
  time to fit residues: 34.6893
Evaluate side-chains
  114 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 30 optimal weight:    0.0270
   chunk 90 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 147 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0770
   chunk 57 optimal weight:    0.0870
   overall best weight:    0.8378

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** 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 = 0.4606 r_free = 0.4606 target = 0.203133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.150261 restraints weight = 14311.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.144115 restraints weight = 9915.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.144514 restraints weight = 9013.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10180  Z= 0.224
  Angle     :  0.630   8.336  13968  Z= 0.335
  Chirality :  0.043   0.151   1712
  Planarity :  0.004   0.051   1826
  Dihedral  :  8.820  81.975   1654
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.60 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.00 %
    Favored  : 82.32 %
  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: -4.79 (0.19), residues: 1462
  helix: -3.34 (0.16), residues: 550
  sheet: -3.38 (0.37), residues: 168
  loop : -2.98 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 529 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.011   0.001   PHE A 471 
 TYR   0.009   0.001   TYR B 171 
 ARG   0.002   0.000   ARG A 335 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8111 (t80) cc_final: 0.7797 (t80)
REVERT: A  194 ASP cc_start: 0.8235 (m-30) cc_final: 0.7966 (m-30)
REVERT: A  204 ILE cc_start: 0.8882 (tp) cc_final: 0.8589 (tp)
REVERT: A  630 PHE cc_start: 0.8413 (m-10) cc_final: 0.8040 (m-80)
REVERT: B  104 TYR cc_start: 0.8082 (t80) cc_final: 0.7765 (t80)
REVERT: B  194 ASP cc_start: 0.8244 (m-30) cc_final: 0.7994 (m-30)
REVERT: B  204 ILE cc_start: 0.8879 (tp) cc_final: 0.8588 (tp)
REVERT: B  630 PHE cc_start: 0.8392 (m-10) cc_final: 0.8016 (m-80)
  outliers start: 22
  outliers final: 20
  residues processed: 127
  average time/residue: 0.1763
  time to fit residues: 34.6782
Evaluate side-chains
  130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  660 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 101 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0170
   chunk 30 optimal weight:    5.9990
   chunk 144 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** 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 = 0.4642 r_free = 0.4642 target = 0.216576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.151022 restraints weight = 14516.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.153849 restraints weight = 9693.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.154184 restraints weight = 7610.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10180  Z= 0.194
  Angle     :  0.606   7.990  13968  Z= 0.321
  Chirality :  0.042   0.148   1712
  Planarity :  0.004   0.050   1826
  Dihedral  :  8.203  81.517   1654
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.68 %
    Favored  : 79.27 %
  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: -4.29 (0.20), residues: 1462
  helix: -2.80 (0.19), residues: 548
  sheet: -3.10 (0.38), residues: 168
  loop : -2.79 (0.21), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 529 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.019   0.001   PHE A 598 
 TYR   0.011   0.001   TYR A 539 
 ARG   0.001   0.000   ARG A 183 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8097 (t80) cc_final: 0.7620 (t80)
REVERT: A  194 ASP cc_start: 0.8231 (m-30) cc_final: 0.7928 (m-30)
REVERT: A  204 ILE cc_start: 0.8837 (tp) cc_final: 0.8537 (tp)
REVERT: A  630 PHE cc_start: 0.8510 (m-10) cc_final: 0.8092 (m-80)
REVERT: B  104 TYR cc_start: 0.8094 (t80) cc_final: 0.7646 (t80)
REVERT: B  194 ASP cc_start: 0.8215 (m-30) cc_final: 0.7961 (m-30)
REVERT: B  204 ILE cc_start: 0.8840 (tp) cc_final: 0.8539 (tp)
REVERT: B  630 PHE cc_start: 0.8512 (m-10) cc_final: 0.8060 (m-80)
  outliers start: 25
  outliers final: 19
  residues processed: 131
  average time/residue: 0.1645
  time to fit residues: 33.7083
Evaluate side-chains
  129 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 125 optimal weight:   20.0000
   chunk 93 optimal weight:    0.0470
   chunk 36 optimal weight:    0.8980
   chunk 113 optimal weight:    0.4980
   chunk 134 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 138 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   chunk 121 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** 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 = 0.4636 r_free = 0.4636 target = 0.208231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.153231 restraints weight = 14238.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.148640 restraints weight = 11042.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.148999 restraints weight = 9050.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10180  Z= 0.172
  Angle     :  0.578   7.157  13968  Z= 0.306
  Chirality :  0.042   0.140   1712
  Planarity :  0.004   0.049   1826
  Dihedral  :  7.720  82.538   1654
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.41 %
    Favored  : 77.68 %
  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: -4.00 (0.20), residues: 1462
  helix: -2.49 (0.20), residues: 552
  sheet: -2.97 (0.39), residues: 170
  loop : -2.68 (0.22), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 529 
 HIS   0.004   0.001   HIS A  94 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.010   0.001   TYR A 539 
 ARG   0.002   0.000   ARG A 335 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8135 (t80) cc_final: 0.7725 (t80)
REVERT: A  194 ASP cc_start: 0.8153 (m-30) cc_final: 0.7833 (m-30)
REVERT: A  630 PHE cc_start: 0.8447 (m-10) cc_final: 0.8040 (m-80)
REVERT: B  104 TYR cc_start: 0.8106 (t80) cc_final: 0.7676 (t80)
REVERT: B  194 ASP cc_start: 0.8150 (m-30) cc_final: 0.7825 (m-30)
REVERT: B  630 PHE cc_start: 0.8428 (m-10) cc_final: 0.8010 (m-80)
  outliers start: 32
  outliers final: 28
  residues processed: 133
  average time/residue: 0.1722
  time to fit residues: 35.3609
Evaluate side-chains
  134 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  527 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 123 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 21 optimal weight:    0.5980
   chunk 115 optimal weight:    0.0870
   chunk 101 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0370
   chunk 73 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    0.9440

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** 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 = 0.4637 r_free = 0.4637 target = 0.215662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.156059 restraints weight = 14640.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.152932 restraints weight = 10060.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.152182 restraints weight = 8558.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10180  Z= 0.238
  Angle     :  0.605   7.411  13968  Z= 0.318
  Chirality :  0.043   0.137   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  7.972  84.962   1654
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.01 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.49 %
    Favored  : 75.73 %
  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: -3.79 (0.21), residues: 1462
  helix: -2.26 (0.21), residues: 558
  sheet: -2.87 (0.39), residues: 168
  loop : -2.61 (0.22), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 529 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.022   0.001   PHE B 598 
 TYR   0.008   0.001   TYR A 539 
 ARG   0.003   0.000   ARG B 206 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 1.089 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8163 (t80) cc_final: 0.7761 (t80)
REVERT: A  194 ASP cc_start: 0.8321 (m-30) cc_final: 0.7971 (m-30)
REVERT: A  630 PHE cc_start: 0.8614 (m-10) cc_final: 0.8162 (m-80)
REVERT: B  104 TYR cc_start: 0.8162 (t80) cc_final: 0.7776 (t80)
REVERT: B  194 ASP cc_start: 0.8314 (m-30) cc_final: 0.7938 (m-30)
REVERT: B  630 PHE cc_start: 0.8593 (m-10) cc_final: 0.8137 (m-80)
  outliers start: 31
  outliers final: 28
  residues processed: 129
  average time/residue: 0.1662
  time to fit residues: 33.1054
Evaluate side-chains
  135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  485 HIS
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  485 HIS
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  527 CYS
Chi-restraints excluded: chain B residue  660 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   chunk 106 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.7362

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** 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 = 0.4622 r_free = 0.4622 target = 0.204696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.146176 restraints weight = 14270.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.147012 restraints weight = 9827.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.146635 restraints weight = 8248.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10180  Z= 0.202
  Angle     :  0.592   6.684  13968  Z= 0.311
  Chirality :  0.042   0.142   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  7.852  88.096   1654
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.71 %
    Favored  : 74.02 %
  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: -3.55 (0.21), residues: 1462
  helix: -2.08 (0.21), residues: 556
  sheet: -2.41 (0.43), residues: 150
  loop : -2.56 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 529 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.007   0.001   TYR A 539 
 ARG   0.003   0.000   ARG A 206 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 108
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8118 (t80) cc_final: 0.7729 (t80)
REVERT: A  194 ASP cc_start: 0.8225 (m-30) cc_final: 0.7878 (m-30)
REVERT: A  630 PHE cc_start: 0.8554 (m-10) cc_final: 0.8113 (m-80)
REVERT: B  104 TYR cc_start: 0.8119 (t80) cc_final: 0.7739 (t80)
REVERT: B  194 ASP cc_start: 0.8208 (m-30) cc_final: 0.7840 (m-30)
REVERT: B  630 PHE cc_start: 0.8538 (m-10) cc_final: 0.8156 (m-80)
  outliers start: 35
  outliers final: 28
  residues processed: 133
  average time/residue: 0.1728
  time to fit residues: 35.5545
Evaluate side-chains
  133 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  527 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 141 optimal weight:   20.0000
   chunk 123 optimal weight:    9.9990
   chunk 98 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 134 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0670
   chunk 70 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 45 optimal weight:   10.0000
   chunk 136 optimal weight:    7.9990
   overall best weight:    1.5520

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 601 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.212578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.148742 restraints weight = 14744.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.149221 restraints weight = 11121.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149680 restraints weight = 7920.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10180  Z= 0.360
  Angle     :  0.656   6.926  13968  Z= 0.343
  Chirality :  0.045   0.137   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  8.528  87.632   1654
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.86 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.95 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.55 (0.21), residues: 1462
  helix: -2.05 (0.21), residues: 558
  sheet: -2.38 (0.43), residues: 148
  loop : -2.59 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 529 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.021   0.002   PHE A 598 
 TYR   0.019   0.002   TYR A 537 
 ARG   0.002   0.000   ARG A 206 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8310 (t80) cc_final: 0.7943 (t80)
REVERT: A  194 ASP cc_start: 0.8267 (m-30) cc_final: 0.7930 (m-30)
REVERT: A  630 PHE cc_start: 0.8503 (m-10) cc_final: 0.8082 (m-80)
REVERT: B  104 TYR cc_start: 0.8309 (t80) cc_final: 0.7950 (t80)
REVERT: B  194 ASP cc_start: 0.8254 (m-30) cc_final: 0.7927 (m-30)
REVERT: B  529 TRP cc_start: 0.7712 (p-90) cc_final: 0.7221 (p-90)
REVERT: B  630 PHE cc_start: 0.8509 (m-10) cc_final: 0.8146 (m-80)
  outliers start: 36
  outliers final: 32
  residues processed: 128
  average time/residue: 0.1718
  time to fit residues: 34.2789
Evaluate side-chains
  135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  485 HIS
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  485 HIS
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  527 CYS
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  771 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 139 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 104 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** 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 = 0.4637 r_free = 0.4637 target = 0.215709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.148624 restraints weight = 14593.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.151339 restraints weight = 9853.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.153310 restraints weight = 7728.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10180  Z= 0.222
  Angle     :  0.602   6.407  13968  Z= 0.316
  Chirality :  0.043   0.149   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  7.925  82.861   1654
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.44 %
    Favored  : 73.90 %
  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: -3.37 (0.21), residues: 1462
  helix: -1.91 (0.22), residues: 554
  sheet: -2.28 (0.43), residues: 148
  loop : -2.48 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 554 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.010   0.001   PHE B 295 
 TYR   0.007   0.001   TYR B 171 
 ARG   0.003   0.000   ARG A 335 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8215 (t80) cc_final: 0.7837 (t80)
REVERT: A  194 ASP cc_start: 0.8218 (m-30) cc_final: 0.7901 (m-30)
REVERT: A  630 PHE cc_start: 0.8692 (m-10) cc_final: 0.8293 (m-80)
REVERT: B  104 TYR cc_start: 0.8222 (t80) cc_final: 0.7848 (t80)
REVERT: B  194 ASP cc_start: 0.8215 (m-30) cc_final: 0.7881 (m-30)
REVERT: B  529 TRP cc_start: 0.7599 (p-90) cc_final: 0.7141 (p-90)
REVERT: B  630 PHE cc_start: 0.8656 (m-10) cc_final: 0.8252 (m-80)
  outliers start: 30
  outliers final: 29
  residues processed: 127
  average time/residue: 0.1871
  time to fit residues: 36.5586
Evaluate side-chains
  130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  485 HIS
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  485 HIS
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  527 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 124 optimal weight:    8.9990
   chunk 147 optimal weight:    0.0670
   chunk 96 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 74 optimal weight:    5.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  94 HIS
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.205819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.152419 restraints weight = 14287.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.146198 restraints weight = 9925.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.146113 restraints weight = 9893.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10180  Z= 0.168
  Angle     :  0.581   6.458  13968  Z= 0.305
  Chirality :  0.042   0.141   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  7.355  76.864   1654
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.41 %
    Favored  : 73.29 %
  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: -3.26 (0.21), residues: 1462
  helix: -1.85 (0.21), residues: 564
  sheet: -2.19 (0.43), residues: 160
  loop : -2.39 (0.22), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 529 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.018   0.001   PHE A 598 
 TYR   0.021   0.001   TYR A 537 
 ARG   0.002   0.000   ARG A 270 

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8164 (t80) cc_final: 0.7842 (t80)
REVERT: A  194 ASP cc_start: 0.8184 (m-30) cc_final: 0.7852 (m-30)
REVERT: A  630 PHE cc_start: 0.8460 (m-10) cc_final: 0.8163 (m-10)
REVERT: B  104 TYR cc_start: 0.8174 (t80) cc_final: 0.7857 (t80)
REVERT: B  194 ASP cc_start: 0.8185 (m-30) cc_final: 0.7863 (m-30)
REVERT: B  529 TRP cc_start: 0.7519 (p-90) cc_final: 0.7257 (p-90)
REVERT: B  630 PHE cc_start: 0.8434 (m-10) cc_final: 0.8094 (m-80)
  outliers start: 27
  outliers final: 22
  residues processed: 125
  average time/residue: 0.1660
  time to fit residues: 31.9708
Evaluate side-chains
  128 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  527 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0670
   chunk 138 optimal weight:    7.9990
   chunk 124 optimal weight:    8.9990
   chunk 32 optimal weight:    0.1980
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 132 optimal weight:    1.9990
   chunk 139 optimal weight:    7.9990
   chunk 147 optimal weight:    0.2980
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.4720 r_free = 0.4720 target = 0.225650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.159162 restraints weight = 14535.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.161966 restraints weight = 9967.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.163976 restraints weight = 7878.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
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Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10180  Z= 0.185
  Angle     :  0.584   6.200  13968  Z= 0.306
  Chirality :  0.042   0.134   1712
  Planarity :  0.003   0.049   1826
  Dihedral  :  7.265  74.095   1654
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.66 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.22), residues: 1462
  helix: -1.78 (0.22), residues: 560
  sheet: -2.14 (0.43), residues: 160
  loop : -2.36 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 554 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.010   0.001   PHE B 295 
 TYR   0.006   0.001   TYR B 431 
 ARG   0.002   0.000   ARG B 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3166.82 seconds
wall clock time: 57 minutes 22.59 seconds (3442.59 seconds total)