Starting phenix.real_space_refine
on Wed Mar 12 20:13:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xt6_33440/03_2025/7xt6_33440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xt6_33440/03_2025/7xt6_33440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2025/7xt6_33440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2025/7xt6_33440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2025/7xt6_33440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2025/7xt6_33440.cif"
  }
  resolution = 3.63
  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=   0.068
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    5067      2.51       5
     N    1342      2.21       5
     O    1591      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8040
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1072
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 11, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2781
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 336}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 1120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1120
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 2785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2785
          Classifications: {'peptide': 364}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 338}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "F"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 64
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "G"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.67, per 1000 atoms: 0.71
  Number of scatterers: 8040
  At special positions: 0
  Unit cell: (71.5, 105.6, 191.4, 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      40     16.00
     O    1591      8.00
     N    1342      7.00
     C    5067      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS C 136 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 270 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS D 350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 380 " - pdb=" SG  CYS B 439 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 487 " - pdb=" SG  CYS B 549 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 122 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 270 " - pdb=" SG  CYS D 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 380 " - pdb=" SG  CYS D 439 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 487 " - pdb=" SG  CYS D 549 " 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
    ALPHA1-3
      " BMA F   3 " - " MAN F   4 "
      " BMA G   3 " - " MAN G   4 "
    BETA1-2
      " MAN F   4 " - " NAG F   5 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG A 201 " - " ASN A  73 "
      " NAG A 202 " - " ASN A  57 "
      " NAG A 203 " - " ASN A  63 "
      " NAG A 204 " - " ASN A  97 "
      " NAG A 205 " - " ASN A  88 "
      " NAG A 206 " - " ASN A 112 "
      " NAG B 701 " - " ASN B 345 "
      " NAG B 702 " - " ASN B 408 "
      " NAG C 201 " - " ASN C 101 "
      " NAG C 202 " - " ASN C  73 "
      " NAG D 701 " - " ASN D 345 "
      " NAG D 702 " - " ASN D 408 "
      " NAG F   1 " - " ASN B 415 "
      " NAG G   1 " - " ASN D 415 "
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 911.7 milliseconds
  

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 24 sheets defined
      19.1% alpha, 25.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 156
      removed outlier: 3.795A  pdb=" N   ASN A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ARG A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 169
      removed outlier: 3.526A  pdb=" N   ARG A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ARG A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 327
    Processing helix  chain 'B' and resid 367 through 372
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.515A  pdb=" N   TRP B 431 " --> pdb=" O   CYS B 427 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY B 434 " --> pdb=" O   ASP B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 478
    Processing helix  chain 'B' and resid 538 through 542
      removed outlier: 3.542A  pdb=" N   ASN B 542 " --> pdb=" O   GLU B 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 538 through 542'
    Processing helix  chain 'B' and resid 581 through 607
      removed outlier: 3.631A  pdb=" N   ALA B 587 " --> pdb=" O   LEU B 583 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   PHE B 594 " --> pdb=" O   PHE B 590 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE B 599 " --> pdb=" O   LEU B 595 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR B 600 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 181
      removed outlier: 3.535A  pdb=" N   LEU C 151 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ILE C 164 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN C 165 " --> pdb=" O   ILE C 161 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR C 166 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
      Proline residue:  C 176  - end of helix
    Processing helix  chain 'D' and resid 322 through 326
    Processing helix  chain 'D' and resid 366 through 374
      removed outlier: 3.569A  pdb=" N   ILE D 370 " --> pdb=" O   SER D 366 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR D 373 " --> pdb=" O   SER D 369 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 428 through 433
      removed outlier: 3.700A  pdb=" N   ASN D 432 " --> pdb=" O   GLU D 428 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 480
      removed outlier: 3.766A  pdb=" N   LEU D 479 " --> pdb=" O   GLU D 475 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG D 480 " --> pdb=" O   GLN D 476 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
      removed outlier: 3.681A  pdb=" N   ASN D 542 " --> pdb=" O   GLU D 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 538 through 542'
    Processing helix  chain 'D' and resid 576 through 608
      removed outlier: 3.662A  pdb=" N   VAL D 592 " --> pdb=" O   SER D 588 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU D 596 " --> pdb=" O   VAL D 592 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   SER D 597 " --> pdb=" O   LEU D 593 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU D 598 " --> pdb=" O   PHE D 594 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44
      removed outlier: 5.807A  pdb=" N   LEU A  42 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51
      removed outlier: 3.812A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 83
      removed outlier: 6.387A  pdb=" N   PHE A  80 " --> pdb=" O   ARG A  68 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ARG A  68 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A  82 " --> pdb=" O   TRP A  66 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE A 103 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 249
      removed outlier: 3.503A  pdb=" N   LYS B 248 " --> pdb=" O   THR B 273 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   THR B 273 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 270
      removed outlier: 3.852A  pdb=" N   SER B 316 " --> pdb=" O   CYS B 270 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 290
    Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 303
    Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 363
      removed outlier: 3.531A  pdb=" N   THR B 379 " --> pdb=" O   ILE B 363 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 394 through 396
    Processing sheet with id=AB1, first strand: chain 'B' and resid 466 through 470
      removed outlier: 3.618A  pdb=" N   THR B 490 " --> pdb=" O   ASP B 466 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   CYS B 487 " --> pdb=" O   SER B 532 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   SER B 532 " --> pdb=" O   CYS B 487 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 498 through 500
      removed outlier: 3.631A  pdb=" N   THR B 561 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 502 through 503
      removed outlier: 3.503A  pdb=" N   GLN B 503 " --> pdb=" O   GLN B 506 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 519 through 520
      removed outlier: 3.648A  pdb=" N   MET B 519 " --> pdb=" O   PHE B 529 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49
    Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56
      removed outlier: 6.693A  pdb=" N   ILE C  53 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   MET C 143 " --> pdb=" O   ILE C  53 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ARG C  55 " --> pdb=" O   MET C 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88
      removed outlier: 3.722A  pdb=" N   TYR C 133 " --> pdb=" O   GLN C 124 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 248 through 252
      removed outlier: 3.810A  pdb=" N   THR D 273 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE D 320 " --> pdb=" O   SER D 266 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 280 through 286
      removed outlier: 3.503A  pdb=" N   CYS D 333 " --> pdb=" O   GLN D 344 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 301 through 302
    Processing sheet with id=AC2, first strand: chain 'D' and resid 360 through 363
      removed outlier: 3.748A  pdb=" N   PHE D 361 " --> pdb=" O   LEU D 381 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR D 379 " --> pdb=" O   ILE D 363 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   THR D 379 " --> pdb=" O   ALA D 424 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ALA D 424 " --> pdb=" O   THR D 379 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   LEU D 381 " --> pdb=" O   GLY D 422 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   GLY D 422 " --> pdb=" O   LEU D 381 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   THR D 383 " --> pdb=" O   ALA D 420 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ALA D 420 " --> pdb=" O   THR D 383 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU D 385 " --> pdb=" O   PHE D 418 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 392 through 396
    Processing sheet with id=AC4, first strand: chain 'D' and resid 466 through 470
      removed outlier: 3.737A  pdb=" N   ASP D 466 " --> pdb=" O   THR D 490 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR D 490 " --> pdb=" O   ASP D 466 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   TYR D 528 " --> pdb=" O   GLY D 491 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 466 through 470
      removed outlier: 3.737A  pdb=" N   ASP D 466 " --> pdb=" O   THR D 490 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR D 490 " --> pdb=" O   ASP D 466 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   TYR D 528 " --> pdb=" O   GLY D 491 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   MET D 519 " --> pdb=" O   PHE D 529 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 506 through 507
      removed outlier: 3.672A  pdb=" N   GLN D 503 " --> pdb=" O   GLN D 506 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR D 561 " --> pdb=" O   VAL D 551 " (cutoff:3.500A)

    253 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: 2.06

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2578
        1.34 -     1.46: 1934
        1.46 -     1.58: 3656
        1.58 -     1.71: 1
        1.71 -     1.83: 56
  Bond restraints: 8225
  Sorted by residual:
  bond pdb=" C1  MAN F   4 "
       pdb=" C2  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.592 -0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" C5  BMA G   3 "
       pdb=" O5  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.462 -0.045 2.00e-02 2.50e+03 5.07e+00
  bond pdb=" C2  MAN F   4 "
       pdb=" C3  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.525  1.569 -0.044 2.00e-02 2.50e+03 4.88e+00
  bond pdb=" C5  BMA F   3 "
       pdb=" O5  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.459 -0.042 2.00e-02 2.50e+03 4.50e+00
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.561 -0.042 2.00e-02 2.50e+03 4.32e+00
  ... (remaining 8220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 11017
        2.68 -     5.35: 166
        5.35 -     8.03: 24
        8.03 -    10.70: 2
       10.70 -    13.38: 2
  Bond angle restraints: 11211
  Sorted by residual:
  angle pdb=" CA  PRO A 129 "
        pdb=" N   PRO A 129 "
        pdb=" CD  PRO A 129 "
      ideal   model   delta    sigma   weight residual
     112.00  105.87    6.13 1.40e+00 5.10e-01 1.91e+01
  angle pdb=" N   PRO A 128 "
        pdb=" CA  PRO A 128 "
        pdb=" C   PRO A 128 "
      ideal   model   delta    sigma   weight residual
     110.70  115.41   -4.71 1.22e+00 6.72e-01 1.49e+01
  angle pdb=" N   GLY C 137 "
        pdb=" CA  GLY C 137 "
        pdb=" C   GLY C 137 "
      ideal   model   delta    sigma   weight residual
     112.22  118.85   -6.63 1.74e+00 3.30e-01 1.45e+01
  angle pdb=" C   VAL B 565 "
        pdb=" N   ASP B 566 "
        pdb=" CA  ASP B 566 "
      ideal   model   delta    sigma   weight residual
     121.90  117.15    4.75 1.26e+00 6.30e-01 1.42e+01
  angle pdb=" CB  PRO A 132 "
        pdb=" CG  PRO A 132 "
        pdb=" CD  PRO A 132 "
      ideal   model   delta    sigma   weight residual
     106.10   94.17   11.93 3.20e+00 9.77e-02 1.39e+01
  ... (remaining 11206 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.86: 4676
       21.86 -    43.71: 441
       43.71 -    65.57: 72
       65.57 -    87.43: 20
       87.43 -   109.28: 14
  Dihedral angle restraints: 5223
    sinusoidal: 2318
      harmonic: 2905
  Sorted by residual:
  dihedral pdb=" CB  CYS B 270 "
           pdb=" SG  CYS B 270 "
           pdb=" SG  CYS B 333 "
           pdb=" CB  CYS B 333 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.25  -85.25     1      1.00e+01 1.00e-02 8.81e+01
  dihedral pdb=" CB  CYS A 119 "
           pdb=" SG  CYS A 119 "
           pdb=" SG  CYS C 136 "
           pdb=" CB  CYS C 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.03  -82.03     1      1.00e+01 1.00e-02 8.27e+01
  dihedral pdb=" CA  ARG A 131 "
           pdb=" C   ARG A 131 "
           pdb=" N   PRO A 132 "
           pdb=" CA  PRO A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -144.79  -35.21     0      5.00e+00 4.00e-02 4.96e+01
  ... (remaining 5220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.144: 1336
       0.144 -    0.289: 9
       0.289 -    0.433: 0
       0.433 -    0.577: 0
       0.577 -    0.721: 1
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN D 415 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.68   -0.72 2.00e-01 2.50e+01 1.30e+01
  chirality pdb=" C1  NAG A 205 "
            pdb=" ND2 ASN A  88 "
            pdb=" C2  NAG A 205 "
            pdb=" O5  NAG A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" C1  NAG A 201 "
            pdb=" ND2 ASN A  73 "
            pdb=" C2  NAG A 201 "
            pdb=" O5  NAG A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1343 not shown)

  Planarity restraints: 1432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 253 "    0.051 5.00e-02 4.00e+02   7.91e-02 1.00e+01
        pdb=" N   PRO B 254 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO B 254 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 254 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 131 "    0.043 5.00e-02 4.00e+02   6.28e-02 6.31e+00
        pdb=" N   PRO A 132 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 132 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 132 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 470 "   -0.041 5.00e-02 4.00e+02   6.26e-02 6.28e+00
        pdb=" N   PRO D 471 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO D 471 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 471 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1429 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 492
        2.73 -     3.27: 7594
        3.27 -     3.81: 12030
        3.81 -     4.36: 13091
        4.36 -     4.90: 23584
  Nonbonded interactions: 56791
  Sorted by model distance:
  nonbonded pdb=" N   GLN D 506 "
            pdb=" OE1 GLN D 506 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" NH2 ARG C  95 "
            pdb=" OD2 ASP C 116 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OG1 THR D 356 "
            pdb=" OD2 ASP D 445 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" N   GLU A 138 "
            pdb=" OE1 GLU A 138 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG1 THR D 373 "
            pdb=" OG  SER D 375 "
     model   vdw
     2.275 3.040
  ... (remaining 56786 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 'B' and (resid 245 through 302 or (resid 303 through 304 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 305 through 352 or (resid 353  \ 
through 355 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 
6 through 357 or (resid 358 through 359 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 360 or (resid 361 through 362 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 363 through 395 or (resid 396 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 397 through 403 or (re \ 
sid 404 and (name N or name CA or name C or name O or name CB )) or resid 405 th \ 
rough 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 414 through 435 or (resid 436 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 437 through 443 or (resid 444 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 445 through 607 or resid 701 through 7 \ 
02))
  selection = (chain 'D' and (resid 245 through 247 or (resid 248 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 249 through 255 or (resid 256 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 257 through 283 or (resid  \ 
284 and (name N or name CA or name C or name O or name CB )) or resid 285 throug \ 
h 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 326 through 331 or (resid 332 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 333 through 347 or (resid 348 through 349 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 350 through 387 or (resid 388  \ 
and (name N or name CA or name C or name O or name CB )) or resid 389 through 41 \ 
6 or (resid 417 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 418 through 607 or resid 701 through 702))
}

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:             3.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     21.600
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
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      :  0.005   0.066   8225  Z= 0.310
  Angle     :  0.814  13.377  11211  Z= 0.408
  Chirality :  0.052   0.721   1346
  Planarity :  0.005   0.079   1418
  Dihedral  : 17.764 109.282   3307
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 24.25 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.27), residues: 995
  helix:  0.97 (0.43), residues: 156
  sheet: -1.19 (0.29), residues: 332
  loop : -2.26 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP D 395 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.017   0.002   PHE B 418 
 TYR   0.013   0.001   TYR D 600 
 ARG   0.003   0.000   ARG B 359 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.887 
Fit side-chains
REVERT: B  454 ILE cc_start: 0.8027 (tp) cc_final: 0.7801 (pt)
REVERT: B  578 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7736 (pt0)
REVERT: D  506 GLN cc_start: 0.7981 (pm20) cc_final: 0.6797 (mm-40)
  outliers start: 7
  outliers final: 2
  residues processed: 81
  average time/residue: 0.2221
  time to fit residues: 24.4535
Evaluate side-chains
  74 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain D residue  431 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0980
   chunk 76 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 281 GLN
** B 337 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 = 0.4282 r_free = 0.4282 target = 0.199464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.129564 restraints weight = 10874.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131712 restraints weight = 8229.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131715 restraints weight = 6785.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8225  Z= 0.227
  Angle     :  0.716  12.444  11211  Z= 0.360
  Chirality :  0.049   0.374   1346
  Planarity :  0.005   0.063   1418
  Dihedral  : 11.732  98.820   1505
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.13 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.27), residues: 995
  helix:  0.77 (0.42), residues: 172
  sheet: -0.88 (0.30), residues: 325
  loop : -2.44 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 395 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.013   0.002   PHE B 418 
 TYR   0.024   0.001   TYR D 547 
 ARG   0.003   0.000   ARG C  55 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: B  454 ILE cc_start: 0.8205 (tp) cc_final: 0.7989 (pt)
REVERT: B  578 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7727 (pt0)
REVERT: C   67 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6761 (ppp)
REVERT: D  469 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8584 (tt)
REVERT: D  506 GLN cc_start: 0.7690 (pm20) cc_final: 0.6923 (mm-40)
  outliers start: 31
  outliers final: 15
  residues processed: 93
  average time/residue: 0.1904
  time to fit residues: 24.9974
Evaluate side-chains
  81 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  469 LEU
Chi-restraints excluded: chain D residue  502 MET
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 443 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.195711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.127038 restraints weight = 10982.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.124221 restraints weight = 8042.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.123700 restraints weight = 7674.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   8225  Z= 0.426
  Angle     :  0.799  11.146  11211  Z= 0.406
  Chirality :  0.052   0.334   1346
  Planarity :  0.006   0.064   1418
  Dihedral  : 10.299  91.803   1503
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 22.74 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.27), residues: 995
  helix:  0.75 (0.42), residues: 172
  sheet: -1.08 (0.29), residues: 329
  loop : -2.59 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 395 
 HIS   0.009   0.002   HIS A  71 
 PHE   0.017   0.002   PHE B 418 
 TYR   0.031   0.002   TYR D 547 
 ARG   0.005   0.001   ARG B 474 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 73
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6985 (tp40) cc_final: 0.5496 (mt0)
REVERT: B  359 ARG cc_start: 0.7377 (mtm180) cc_final: 0.6715 (mtm180)
REVERT: B  470 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8527 (mt)
REVERT: D  469 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8681 (tt)
  outliers start: 57
  outliers final: 34
  residues processed: 120
  average time/residue: 0.2062
  time to fit residues: 35.8794
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 66
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  599 PHE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  469 LEU
Chi-restraints excluded: chain D residue  502 MET
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0870
   chunk 36 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4260 r_free = 0.4260 target = 0.197457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 121)---------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.130714 restraints weight = 11033.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.126627 restraints weight = 8277.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128759 restraints weight = 7733.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8225  Z= 0.227
  Angle     :  0.688   9.076  11211  Z= 0.346
  Chirality :  0.048   0.389   1346
  Planarity :  0.005   0.070   1418
  Dihedral  :  9.337  86.699   1503
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 23.90 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.27), residues: 995
  helix:  0.81 (0.41), residues: 169
  sheet: -0.93 (0.29), residues: 326
  loop : -2.48 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 395 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.013   0.001   PHE B 498 
 TYR   0.030   0.001   TYR D 547 
 ARG   0.004   0.000   ARG B 474 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 66
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6755 (tp40) cc_final: 0.5365 (mt0)
REVERT: B  407 THR cc_start: 0.4302 (OUTLIER) cc_final: 0.3998 (p)
REVERT: C   67 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6695 (ppp)
REVERT: D  581 GLU cc_start: 0.7449 (tp30) cc_final: 0.7221 (mm-30)
  outliers start: 48
  outliers final: 31
  residues processed: 104
  average time/residue: 0.1797
  time to fit residues: 27.1815
Evaluate side-chains
  94 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 61
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  415 ASN
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  454 ILE
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  589 THR
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    0.1980
   chunk 79 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 92 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4320 r_free = 0.4320 target = 0.201381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.152775 restraints weight = 10732.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.134818 restraints weight = 15471.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.136107 restraints weight = 12351.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8225  Z= 0.233
  Angle     :  0.689   8.559  11211  Z= 0.345
  Chirality :  0.048   0.343   1346
  Planarity :  0.005   0.070   1418
  Dihedral  :  8.701  80.426   1503
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 22.62 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.27), residues: 995
  helix:  0.89 (0.42), residues: 169
  sheet: -0.83 (0.30), residues: 312
  loop : -2.45 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 395 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.013   0.001   PHE B 492 
 TYR   0.029   0.002   TYR D 547 
 ARG   0.003   0.000   ARG B 474 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 64
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6743 (tp40) cc_final: 0.5347 (mt0)
REVERT: B  599 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7283 (m-10)
REVERT: C   67 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6753 (ppp)
REVERT: D  469 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8412 (tt)
  outliers start: 52
  outliers final: 35
  residues processed: 106
  average time/residue: 0.1686
  time to fit residues: 26.2743
Evaluate side-chains
  103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 65
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  599 PHE
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  415 ASN
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  469 LEU
Chi-restraints excluded: chain D residue  502 MET
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  589 THR
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 71 optimal weight:    9.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4314 r_free = 0.4314 target = 0.200778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.153614 restraints weight = 10705.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.141530 restraints weight = 16940.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.134870 restraints weight = 10629.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8225  Z= 0.253
  Angle     :  0.704  10.976  11211  Z= 0.350
  Chirality :  0.050   0.459   1346
  Planarity :  0.005   0.071   1418
  Dihedral  :  8.085  72.953   1501
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 23.32 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.27), residues: 995
  helix:  1.02 (0.42), residues: 169
  sheet: -0.82 (0.30), residues: 314
  loop : -2.39 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 395 
 HIS   0.006   0.001   HIS A  71 
 PHE   0.020   0.002   PHE B 418 
 TYR   0.026   0.002   TYR D 547 
 ARG   0.003   0.000   ARG B 474 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 66
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6831 (tp40) cc_final: 0.5372 (mt0)
REVERT: B  359 ARG cc_start: 0.7075 (mtm180) cc_final: 0.6834 (mtm180)
REVERT: B  599 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7252 (m-10)
REVERT: C   67 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6756 (ppp)
REVERT: D  506 GLN cc_start: 0.7716 (pm20) cc_final: 0.7031 (mm-40)
REVERT: D  547 TYR cc_start: 0.8697 (m-80) cc_final: 0.8481 (m-80)
  outliers start: 48
  outliers final: 37
  residues processed: 105
  average time/residue: 0.1603
  time to fit residues: 24.6419
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 65
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  599 PHE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  415 ASN
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  502 MET
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  589 THR
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Chi-restraints excluded: chain D residue  606 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0470
   chunk 35 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0370
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4330 r_free = 0.4330 target = 0.202475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.170155 restraints weight = 10711.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.162379 restraints weight = 26089.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.157552 restraints weight = 13693.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8225  Z= 0.200
  Angle     :  0.668   8.512  11211  Z= 0.332
  Chirality :  0.047   0.343   1346
  Planarity :  0.005   0.070   1418
  Dihedral  :  7.440  65.701   1501
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.48 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.27), residues: 995
  helix:  1.05 (0.42), residues: 169
  sheet: -0.74 (0.30), residues: 313
  loop : -2.31 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP D 395 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.012   0.001   PHE B 498 
 TYR   0.024   0.001   TYR D 547 
 ARG   0.005   0.000   ARG A 126 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 74
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6610 (tp40) cc_final: 0.5287 (mt0)
REVERT: A  126 ARG cc_start: 0.6169 (pmt-80) cc_final: 0.5789 (pmt-80)
REVERT: B  599 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7432 (m-10)
REVERT: C   67 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6652 (ppp)
REVERT: C  165 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7189 (mt0)
REVERT: D  547 TYR cc_start: 0.8679 (m-80) cc_final: 0.8455 (m-80)
  outliers start: 41
  outliers final: 32
  residues processed: 105
  average time/residue: 0.1781
  time to fit residues: 26.8540
Evaluate side-chains
  106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 71
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  599 PHE
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  415 ASN
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  589 THR
Chi-restraints excluded: chain D residue  598 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 68 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4317 r_free = 0.4317 target = 0.201096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.154199 restraints weight = 10856.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.138125 restraints weight = 15810.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133302 restraints weight = 11114.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8225  Z= 0.254
  Angle     :  0.700   9.587  11211  Z= 0.350
  Chirality :  0.049   0.335   1346
  Planarity :  0.005   0.069   1418
  Dihedral  :  7.143  60.199   1501
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 24.13 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.27), residues: 995
  helix:  1.10 (0.42), residues: 169
  sheet: -0.74 (0.30), residues: 313
  loop : -2.34 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP D 395 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.012   0.001   PHE B 498 
 TYR   0.021   0.001   TYR D 547 
 ARG   0.006   0.000   ARG A 126 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 66
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6840 (tp40) cc_final: 0.5407 (mt0)
REVERT: A  117 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8610 (tt0)
REVERT: A  126 ARG cc_start: 0.6420 (pmt-80) cc_final: 0.6070 (pmt-80)
REVERT: B  599 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7220 (m-10)
REVERT: C   67 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6702 (ppp)
REVERT: C  165 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7154 (mt0)
  outliers start: 46
  outliers final: 36
  residues processed: 101
  average time/residue: 0.1665
  time to fit residues: 24.4116
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 64
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  117 GLN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  599 PHE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  460 VAL
Chi-restraints excluded: chain D residue  502 MET
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  589 THR
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  606 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 76 optimal weight:    0.0170
   chunk 43 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4335 r_free = 0.4335 target = 0.203108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.170777 restraints weight = 10899.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.165126 restraints weight = 26225.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.160373 restraints weight = 14252.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8225  Z= 0.185
  Angle     :  0.683  11.640  11211  Z= 0.335
  Chirality :  0.047   0.387   1346
  Planarity :  0.005   0.065   1418
  Dihedral  :  6.789  53.695   1501
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.48 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.27), residues: 995
  helix:  1.12 (0.42), residues: 169
  sheet: -0.61 (0.30), residues: 313
  loop : -2.30 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP D 395 
 HIS   0.003   0.001   HIS A  71 
 PHE   0.012   0.001   PHE B 498 
 TYR   0.034   0.001   TYR D 547 
 ARG   0.005   0.000   ARG A 126 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 68
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6464 (tp40) cc_final: 0.5197 (mt0)
REVERT: A  126 ARG cc_start: 0.6188 (pmt-80) cc_final: 0.5984 (pmt-80)
REVERT: C   67 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6660 (ppp)
REVERT: C  165 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7343 (mt0)
  outliers start: 41
  outliers final: 35
  residues processed: 101
  average time/residue: 0.1686
  time to fit residues: 24.7043
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  438 THR
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Chi-restraints excluded: chain D residue  606 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 56 optimal weight:    0.0870
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4324 r_free = 0.4324 target = 0.201877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.155529 restraints weight = 10755.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.145269 restraints weight = 16357.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.140956 restraints weight = 10759.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8225  Z= 0.228
  Angle     :  0.695   9.680  11211  Z= 0.344
  Chirality :  0.048   0.446   1346
  Planarity :  0.005   0.058   1418
  Dihedral  :  6.597  53.523   1501
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 24.25 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.27), residues: 995
  helix:  1.16 (0.42), residues: 169
  sheet: -0.60 (0.30), residues: 318
  loop : -2.28 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP D 395 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.012   0.001   PHE B 498 
 TYR   0.010   0.001   TYR D 600 
 ARG   0.005   0.000   ARG A 126 

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 66
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.6732 (tp40) cc_final: 0.5289 (mt0)
REVERT: B  359 ARG cc_start: 0.7107 (ptp-170) cc_final: 0.6512 (mtm180)
REVERT: B  599 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7311 (m-10)
REVERT: C   67 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6757 (ppp)
  outliers start: 40
  outliers final: 35
  residues processed: 99
  average time/residue: 0.1679
  time to fit residues: 24.1282
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 65
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  438 THR
Chi-restraints excluded: chain B residue  439 CYS
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  519 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  599 PHE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  123 GLN
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  370 ILE
Chi-restraints excluded: chain D residue  391 VAL
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  588 SER
Chi-restraints excluded: chain D residue  589 THR
Chi-restraints excluded: chain D residue  598 LEU
Chi-restraints excluded: chain D residue  605 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0170
   chunk 32 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 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 = 0.4323 r_free = 0.4323 target = 0.201799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.155036 restraints weight = 10817.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.145076 restraints weight = 16261.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.136305 restraints weight = 10372.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8225  Z= 0.231
  Angle     :  0.688   8.540  11211  Z= 0.343
  Chirality :  0.048   0.423   1346
  Planarity :  0.005   0.084   1418
  Dihedral  :  6.349  50.812   1501
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 24.01 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.94 %
    Cis-general     : 0.11 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.27), residues: 995
  helix:  1.14 (0.42), residues: 169
  sheet: -0.58 (0.30), residues: 318
  loop : -2.28 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP D 395 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.014   0.001   PHE D 342 
 TYR   0.035   0.002   TYR D 547 
 ARG   0.003   0.000   ARG A 126 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2856.43 seconds
wall clock time: 51 minutes 6.20 seconds (3066.20 seconds total)