Starting phenix.real_space_refine
on Wed Sep 25 11:57:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/09_2024/7wih_32530.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/09_2024/7wih_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/09_2024/7wih_32530.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/09_2024/7wih_32530.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/09_2024/7wih_32530.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/09_2024/7wih_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-5461/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: 10.00, 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: 2.29
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.17
  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: 2.79

  Time building geometry restraints manager: 2.64 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: 0.00
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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.110
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.380
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 1.306 
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: 0.1908
  time to fit residues: 40.5527
Evaluate side-chains
  105 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
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 fitting.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 ASP cc_start: 0.7997 (m-30) cc_final: 0.7767 (m-30)
REVERT: A  204 ILE cc_start: 0.8940 (tp) cc_final: 0.8642 (tp)
REVERT: A  630 PHE cc_start: 0.8499 (m-10) cc_final: 0.8088 (m-80)
REVERT: B  194 ASP cc_start: 0.7990 (m-30) cc_final: 0.7779 (m-30)
REVERT: B  204 ILE cc_start: 0.8896 (tp) cc_final: 0.8581 (tp)
REVERT: B  260 ILE cc_start: 0.8528 (tp) cc_final: 0.8327 (tp)
REVERT: B  630 PHE cc_start: 0.8451 (m-10) cc_final: 0.8028 (m-80)
  outliers start: 21
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1771
  time to fit residues: 33.2056
Evaluate side-chains
  115 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
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 74 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0570
   chunk 111 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 134 optimal weight:    8.9990
   chunk 145 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 133 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.5104

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10180  Z= 0.349
  Angle     :  0.691   9.150  13968  Z= 0.365
  Chirality :  0.045   0.164   1712
  Planarity :  0.005   0.051   1826
  Dihedral  :  9.587  85.013   1654
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.86 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.63 %
    Favored  : 81.83 %
  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: -4.86 (0.19), residues: 1462
  helix: -3.36 (0.16), residues: 552
  sheet: -3.42 (0.37), residues: 168
  loop : -3.04 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 529 
 HIS   0.005   0.001   HIS A 485 
 PHE   0.021   0.002   PHE A 471 
 TYR   0.012   0.002   TYR B 466 
 ARG   0.002   0.000   ARG A 183 

*********************** 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 fitting.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8197 (t80) cc_final: 0.7840 (t80)
REVERT: A  107 GLU cc_start: 0.7885 (tp30) cc_final: 0.7666 (tp30)
REVERT: A  194 ASP cc_start: 0.8124 (m-30) cc_final: 0.7850 (m-30)
REVERT: A  204 ILE cc_start: 0.8917 (tp) cc_final: 0.8620 (tp)
REVERT: A  630 PHE cc_start: 0.8519 (m-10) cc_final: 0.8111 (m-80)
REVERT: B  104 TYR cc_start: 0.8200 (t80) cc_final: 0.7843 (t80)
REVERT: B  194 ASP cc_start: 0.8116 (m-30) cc_final: 0.7875 (m-30)
REVERT: B  204 ILE cc_start: 0.8919 (tp) cc_final: 0.8622 (tp)
REVERT: B  630 PHE cc_start: 0.8552 (m-10) cc_final: 0.8140 (m-80)
  outliers start: 29
  outliers final: 27
  residues processed: 124
  average time/residue: 0.1639
  time to fit residues: 31.5354
Evaluate side-chains
  127 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   79 ILE
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  435 LEU
Chi-restraints excluded: chain B residue  454 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 133 optimal weight:   10.0000
   chunk 101 optimal weight:    0.4980
   chunk 69 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 135 optimal weight:    0.0010
   chunk 143 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 128 optimal weight:   30.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.8390

-------------------------------------------------------------------------------
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**
B 766 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10180  Z= 0.221
  Angle     :  0.628   8.368  13968  Z= 0.333
  Chirality :  0.043   0.162   1712
  Planarity :  0.004   0.050   1826
  Dihedral  :  8.908  86.117   1654
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.68 %
    Favored  : 78.54 %
  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: -4.41 (0.20), residues: 1462
  helix: -2.86 (0.18), residues: 556
  sheet: -3.25 (0.38), residues: 170
  loop : -2.88 (0.21), residues: 736

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   0.019   0.001   PHE B 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
  137 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8059 (t80) cc_final: 0.7711 (t80)
REVERT: A  194 ASP cc_start: 0.8051 (m-30) cc_final: 0.7785 (m-30)
REVERT: A  204 ILE cc_start: 0.8931 (tp) cc_final: 0.8676 (tp)
REVERT: A  630 PHE cc_start: 0.8520 (m-10) cc_final: 0.8120 (m-80)
REVERT: B  104 TYR cc_start: 0.8061 (t80) cc_final: 0.7718 (t80)
REVERT: B  194 ASP cc_start: 0.8087 (m-30) cc_final: 0.7837 (m-30)
REVERT: B  204 ILE cc_start: 0.8933 (tp) cc_final: 0.8678 (tp)
REVERT: B  598 PHE cc_start: 0.8101 (m-80) cc_final: 0.7884 (m-80)
REVERT: B  630 PHE cc_start: 0.8506 (m-10) cc_final: 0.8065 (m-80)
  outliers start: 31
  outliers final: 24
  residues processed: 128
  average time/residue: 0.1629
  time to fit residues: 32.5687
Evaluate side-chains
  128 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
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  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  527 CYS
Chi-restraints excluded: chain A residue  771 ILE
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  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  771 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 122 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0060
   chunk 128 optimal weight:   40.0000
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.4004

-------------------------------------------------------------------------------
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**
B 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10180  Z= 0.327
  Angle     :  0.660   8.672  13968  Z= 0.347
  Chirality :  0.044   0.165   1712
  Planarity :  0.004   0.049   1826
  Dihedral  :  9.202  89.861   1654
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.20 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 19.76 %
    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: -4.18 (0.20), residues: 1462
  helix: -2.60 (0.20), residues: 556
  sheet: -3.09 (0.39), residues: 168
  loop : -2.82 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 529 
 HIS   0.004   0.001   HIS B 485 
 PHE   0.017   0.002   PHE B 471 
 TYR   0.011   0.002   TYR A 539 
 ARG   0.003   0.000   ARG B 206 

*********************** 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
  137 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8215 (t80) cc_final: 0.7918 (t80)
REVERT: A  194 ASP cc_start: 0.8131 (m-30) cc_final: 0.7814 (m-30)
REVERT: A  204 ILE cc_start: 0.8988 (tp) cc_final: 0.8727 (tp)
REVERT: A  598 PHE cc_start: 0.8085 (m-80) cc_final: 0.7827 (m-80)
REVERT: A  630 PHE cc_start: 0.8575 (m-10) cc_final: 0.8149 (m-80)
REVERT: B  104 TYR cc_start: 0.8216 (t80) cc_final: 0.7921 (t80)
REVERT: B  194 ASP cc_start: 0.8130 (m-30) cc_final: 0.7825 (m-30)
REVERT: B  204 ILE cc_start: 0.8983 (tp) cc_final: 0.8718 (tp)
REVERT: B  630 PHE cc_start: 0.8559 (m-10) cc_final: 0.8132 (m-80)
  outliers start: 37
  outliers final: 29
  residues processed: 125
  average time/residue: 0.1867
  time to fit residues: 36.0972
Evaluate side-chains
  127 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
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  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  660 LEU
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  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  518 MET
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  771 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 128 optimal weight:   30.0000
   chunk 28 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 143 optimal weight:   10.0000
   chunk 118 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    1.2184

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10180  Z= 0.289
  Angle     :  0.640   7.950  13968  Z= 0.337
  Chirality :  0.044   0.168   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  9.065  85.960   1654
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.70 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 20.12 %
    Favored  : 75.24 %
  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: -3.99 (0.20), residues: 1462
  helix: -2.39 (0.20), residues: 558
  sheet: -3.02 (0.38), residues: 180
  loop : -2.72 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 529 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.013   0.002   PHE B 471 
 TYR   0.010   0.001   TYR A 539 
 ARG   0.004   0.000   ARG A 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
  141 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 103
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8122 (t80) cc_final: 0.7815 (t80)
REVERT: A  186 TYR cc_start: 0.8997 (m-80) cc_final: 0.8782 (m-80)
REVERT: A  194 ASP cc_start: 0.8090 (m-30) cc_final: 0.7782 (m-30)
REVERT: A  204 ILE cc_start: 0.9021 (tp) cc_final: 0.8766 (tp)
REVERT: A  630 PHE cc_start: 0.8593 (m-10) cc_final: 0.8157 (m-80)
REVERT: B  104 TYR cc_start: 0.8125 (t80) cc_final: 0.7819 (t80)
REVERT: B  186 TYR cc_start: 0.8995 (m-80) cc_final: 0.8778 (m-80)
REVERT: B  194 ASP cc_start: 0.8090 (m-30) cc_final: 0.7786 (m-30)
REVERT: B  204 ILE cc_start: 0.9014 (tp) cc_final: 0.8760 (tp)
REVERT: B  598 PHE cc_start: 0.8157 (m-80) cc_final: 0.7954 (m-80)
REVERT: B  630 PHE cc_start: 0.8575 (m-10) cc_final: 0.8134 (m-80)
  outliers start: 38
  outliers final: 31
  residues processed: 128
  average time/residue: 0.1641
  time to fit residues: 32.4731
Evaluate side-chains
  132 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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  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  425 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 A residue  660 LEU
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  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  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
Chi-restraints excluded: chain B residue  771 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 138 optimal weight:    0.0670
   chunk 16 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   chunk 120 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 142 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.6720

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2729

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= 0.191
  Angle     :  0.601   6.998  13968  Z= 0.317
  Chirality :  0.043   0.166   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  8.255  81.239   1654
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.94 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.20 %
    Favored  : 74.15 %
  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: -3.75 (0.21), residues: 1462
  helix: -2.18 (0.21), residues: 558
  sheet: -2.83 (0.39), residues: 180
  loop : -2.62 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 529 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.017   0.001   PHE A 598 
 TYR   0.007   0.001   TYR A 336 
 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
  139 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7949 (t80) cc_final: 0.7714 (t80)
REVERT: A  194 ASP cc_start: 0.8073 (m-30) cc_final: 0.7760 (m-30)
REVERT: A  204 ILE cc_start: 0.8981 (tp) cc_final: 0.8716 (tp)
REVERT: A  630 PHE cc_start: 0.8603 (m-10) cc_final: 0.8145 (m-80)
REVERT: B  104 TYR cc_start: 0.7955 (t80) cc_final: 0.7715 (t80)
REVERT: B  194 ASP cc_start: 0.8049 (m-30) cc_final: 0.7738 (m-30)
REVERT: B  204 ILE cc_start: 0.8977 (tp) cc_final: 0.8706 (tp)
REVERT: B  529 TRP cc_start: 0.7614 (p-90) cc_final: 0.7267 (p-90)
REVERT: B  598 PHE cc_start: 0.8076 (m-80) cc_final: 0.7859 (m-80)
REVERT: B  630 PHE cc_start: 0.8583 (m-10) cc_final: 0.8124 (m-80)
  outliers start: 30
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1755
  time to fit residues: 34.8850
Evaluate side-chains
  129 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 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  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 B residue   44 LEU
Chi-restraints excluded: chain B residue   73 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  323 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  425 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0970
   chunk 90 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 70 optimal weight:    6.9990
   chunk 13 optimal weight:    0.2980
   chunk 112 optimal weight:    0.6980
   chunk 129 optimal weight:    9.9990
   overall best weight:    0.3576

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10180  Z= 0.147
  Angle     :  0.585   6.490  13968  Z= 0.308
  Chirality :  0.042   0.155   1712
  Planarity :  0.004   0.049   1826
  Dihedral  :  7.427  74.972   1654
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.17 %
    Favored  : 73.54 %
  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: -3.48 (0.21), residues: 1462
  helix: -1.99 (0.21), residues: 556
  sheet: -2.25 (0.43), residues: 160
  loop : -2.57 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 529 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.007   0.001   TYR B 539 
 ARG   0.002   0.000   ARG B 277 

*********************** 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
  143 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 1.109 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7913 (t80) cc_final: 0.7690 (t80)
REVERT: A  194 ASP cc_start: 0.8033 (m-30) cc_final: 0.7709 (m-30)
REVERT: A  630 PHE cc_start: 0.8616 (m-10) cc_final: 0.8220 (m-80)
REVERT: B  104 TYR cc_start: 0.7924 (t80) cc_final: 0.7701 (t80)
REVERT: B  194 ASP cc_start: 0.8031 (m-30) cc_final: 0.7707 (m-30)
REVERT: B  598 PHE cc_start: 0.8110 (m-80) cc_final: 0.7902 (m-80)
REVERT: B  630 PHE cc_start: 0.8621 (m-10) cc_final: 0.8223 (m-80)
  outliers start: 27
  outliers final: 23
  residues processed: 137
  average time/residue: 0.1796
  time to fit residues: 37.5398
Evaluate side-chains
  136 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
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  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  377 LEU
Chi-restraints excluded: chain A residue  425 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   73 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  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 132 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0970
   chunk 57 optimal weight:    8.9990
   chunk 104 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 120 optimal weight:    0.6980
   chunk 125 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 140 optimal weight:   20.0000
   overall best weight:    1.9584

-------------------------------------------------------------------------------
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 156 GLN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  10180  Z= 0.434
  Angle     :  0.709   7.463  13968  Z= 0.369
  Chirality :  0.047   0.160   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  8.802  75.667   1654
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.41 %
    Favored  : 86.59 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 23.05 %
    Favored  : 72.80 %
  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: -3.52 (0.21), residues: 1462
  helix: -1.99 (0.21), residues: 556
  sheet: -2.45 (0.43), residues: 148
  loop : -2.59 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP B 529 
 HIS   0.004   0.002   HIS B 485 
 PHE   0.019   0.002   PHE A 598 
 TYR   0.018   0.002   TYR B 150 
 ARG   0.005   0.001   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
  141 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8246 (t80) cc_final: 0.7933 (t80)
REVERT: A  194 ASP cc_start: 0.8164 (m-30) cc_final: 0.7866 (m-30)
REVERT: A  630 PHE cc_start: 0.8653 (m-10) cc_final: 0.8283 (m-10)
REVERT: B  104 TYR cc_start: 0.8254 (t80) cc_final: 0.7945 (t80)
REVERT: B  194 ASP cc_start: 0.8164 (m-30) cc_final: 0.7870 (m-30)
REVERT: B  598 PHE cc_start: 0.8086 (m-80) cc_final: 0.7877 (m-80)
REVERT: B  630 PHE cc_start: 0.8663 (m-10) cc_final: 0.8316 (m-10)
  outliers start: 34
  outliers final: 27
  residues processed: 132
  average time/residue: 0.1772
  time to fit residues: 35.5656
Evaluate side-chains
  131 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
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  245 GLU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  425 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  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  323 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 85 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 147 optimal weight:    0.0270
   chunk 135 optimal weight:   20.0000
   chunk 117 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0980
   chunk 125 optimal weight:    8.9990
   overall best weight:    0.4238

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10180  Z= 0.165
  Angle     :  0.608   7.416  13968  Z= 0.318
  Chirality :  0.042   0.169   1712
  Planarity :  0.004   0.049   1826
  Dihedral  :  7.600  70.012   1654
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 24.02 %
    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: -3.33 (0.21), residues: 1462
  helix: -1.82 (0.22), residues: 552
  sheet: -2.26 (0.43), residues: 160
  loop : -2.50 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 486 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.011   0.001   PHE B 295 
 TYR   0.014   0.001   TYR B 186 
 ARG   0.002   0.000   ARG A 206 

********************** 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
  133 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 1.097 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7995 (t80) cc_final: 0.7738 (t80)
REVERT: A  194 ASP cc_start: 0.8085 (m-30) cc_final: 0.7778 (m-30)
REVERT: A  630 PHE cc_start: 0.8666 (m-10) cc_final: 0.8306 (m-10)
REVERT: B  104 TYR cc_start: 0.8003 (t80) cc_final: 0.7749 (t80)
REVERT: B  194 ASP cc_start: 0.8062 (m-30) cc_final: 0.7762 (m-30)
REVERT: B  598 PHE cc_start: 0.8097 (m-80) cc_final: 0.7855 (m-80)
REVERT: B  630 PHE cc_start: 0.8638 (m-10) cc_final: 0.8277 (m-10)
  outliers start: 24
  outliers final: 22
  residues processed: 126
  average time/residue: 0.1760
  time to fit residues: 34.2117
Evaluate side-chains
  130 residues out of total 1290 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
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  245 GLU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  425 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  323 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  485 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 108 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 117 optimal weight:    0.4980
   chunk 49 optimal weight:    9.9990
   chunk 120 optimal weight:    4.9990
   chunk 14 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A  94 HIS

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 = 0.205637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.153542 restraints weight = 14067.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.147686 restraints weight = 10211.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.147855 restraints weight = 9322.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.3295

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= 0.168
  Angle     :  0.590   7.263  13968  Z= 0.308
  Chirality :  0.042   0.160   1712
  Planarity :  0.004   0.049   1826
  Dihedral  :  7.051  64.064   1654
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.54 %
    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: -3.22 (0.22), residues: 1462
  helix: -1.76 (0.22), residues: 562
  sheet: -2.16 (0.43), residues: 160
  loop : -2.43 (0.22), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 486 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.016   0.001   PHE A 598 
 TYR   0.009   0.001   TYR B 186 
 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: 1948.98 seconds
wall clock time: 36 minutes 2.28 seconds (2162.28 seconds total)