Starting phenix.real_space_refine
on Thu Jul 31 18:55:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fhk_31585/07_2025/7fhk_31585.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fhk_31585/07_2025/7fhk_31585.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2025/7fhk_31585.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2025/7fhk_31585.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2025/7fhk_31585.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2025/7fhk_31585.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3394 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      44      5.16       5
     C    7346      2.51       5
     N    1710      2.21       5
     O    1954      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11058
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5467
          Classifications: {'peptide': 663}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 20, 'TRANS': 642}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 60
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'UNK:plan-1': 12}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 5467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5467
          Classifications: {'peptide': 663}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 20, 'TRANS': 642}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 60
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'UNK:plan-1': 12}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.79, per 1000 atoms: 0.61
  Number of scatterers: 11058
  At special positions: 0
  Unit cell: (88.218, 120.666, 116.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      44     16.00
     O    1954      8.00
     N    1710      7.00
     C    7346      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.00
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2584

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 0 sheets defined
      87.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 27
    Processing helix  chain 'A' and resid 29 through 44
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 57 through 69
      removed outlier: 3.520A  pdb=" N   ALA A  61 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 88
      removed outlier: 3.525A  pdb=" N   TRP A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   ASN A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   PHE A  86 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   PHE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 95
      removed outlier: 3.766A  pdb=" N   GLU A  94 " --> pdb=" O   PRO A  90 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 95'
    Processing helix  chain 'A' and resid 116 through 137
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 143 through 150
      removed outlier: 3.616A  pdb=" N   SER A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 174
    Processing helix  chain 'A' and resid 186 through 197
      removed outlier: 3.598A  pdb=" N   VAL A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 238
      removed outlier: 4.295A  pdb=" N   GLY A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 222 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.503A  pdb=" N   LEU A 245 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.769A  pdb=" N   THR A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
      removed outlier: 3.937A  pdb=" N   VAL A 270 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TRP A 271 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 266 through 271'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 281 through 295
      removed outlier: 3.719A  pdb=" N   PHE A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 335
    Processing helix  chain 'A' and resid 343 through 358
      removed outlier: 3.857A  pdb=" N   LYS A 349 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 376
      removed outlier: 4.231A  pdb=" N   GLY A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASP A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 399
      removed outlier: 3.772A  pdb=" N   ALA A 389 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASP A 390 " --> pdb=" O   ASP A 386 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU A 391 " --> pdb=" O   GLU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 429
    Processing helix  chain 'A' and resid 429 through 456
      removed outlier: 3.964A  pdb=" N   GLY A 433 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 487
      removed outlier: 4.058A  pdb=" N   TRP A 464 " --> pdb=" O   ALA A 460 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY A 472 " --> pdb=" O   GLU A 468 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 494
      removed outlier: 4.209A  pdb=" N   GLU A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 517
    Processing helix  chain 'A' and resid 528 through 538
      removed outlier: 4.377A  pdb=" N   TYR A 532 " --> pdb=" O   GLU A 528 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 533 " --> pdb=" O   TRP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
    Processing helix  chain 'A' and resid 551 through 565
      Proline residue:  A 563  - end of helix
    Processing helix  chain 'A' and resid 565 through 587
    Processing helix  chain 'A' and resid 595 through 601
      removed outlier: 4.047A  pdb=" N   PHE A 599 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU A 600 " --> pdb=" O   LYS A 596 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR A 601 " --> pdb=" O   LYS A 597 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 595 through 601'
    Processing helix  chain 'A' and resid 601 through 607
      removed outlier: 3.786A  pdb=" N   GLU A 605 " --> pdb=" O   THR A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 612
    Processing helix  chain 'A' and resid 615 through 628
    Processing helix  chain 'A' and resid 632 through 644
      removed outlier: 3.957A  pdb=" N   MET A 636 " --> pdb=" O   TRP A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 647
      No H-bonds generated for 'chain 'A' and resid 645 through 647'
    Processing helix  chain 'A' and resid 648 through 660
      removed outlier: 3.957A  pdb=" N   PHE A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 686
      removed outlier: 3.601A  pdb=" N   LEU A 681 " --> pdb=" O   THR A 677 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 685 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LYS A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 17
    Processing helix  chain 'C' and resid 20 through 27
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 48 through 54
    Processing helix  chain 'C' and resid 57 through 69
      removed outlier: 3.517A  pdb=" N   ALA C  61 " --> pdb=" O   PHE C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 88
      removed outlier: 3.511A  pdb=" N   TRP C  74 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ASN C  85 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   PHE C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   PHE C  87 " --> pdb=" O   PHE C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 95
      removed outlier: 3.749A  pdb=" N   GLU C  94 " --> pdb=" O   PRO C  90 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS C  95 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 90 through 95'
    Processing helix  chain 'C' and resid 116 through 137
    Processing helix  chain 'C' and resid 138 through 143
    Processing helix  chain 'C' and resid 143 through 150
      removed outlier: 3.552A  pdb=" N   THR C 149 " --> pdb=" O   ARG C 145 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER C 150 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 174
    Processing helix  chain 'C' and resid 186 through 199
      removed outlier: 3.775A  pdb=" N   ILE C 199 " --> pdb=" O   PHE C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 238
      removed outlier: 4.930A  pdb=" N   GLY C 214 " --> pdb=" O   SER C 210 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   THR C 215 " --> pdb=" O   GLY C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 247
    Processing helix  chain 'C' and resid 250 through 264
    Processing helix  chain 'C' and resid 266 through 271
      removed outlier: 3.944A  pdb=" N   VAL C 270 " --> pdb=" O   ASN C 266 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   TRP C 271 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 266 through 271'
    Processing helix  chain 'C' and resid 271 through 278
    Processing helix  chain 'C' and resid 280 through 295
      removed outlier: 4.208A  pdb=" N   PHE C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU C 290 " --> pdb=" O   VAL C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 335
    Processing helix  chain 'C' and resid 343 through 358
    Processing helix  chain 'C' and resid 364 through 376
      removed outlier: 3.505A  pdb=" N   PHE C 368 " --> pdb=" O   SER C 364 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLY C 369 " --> pdb=" O   LYS C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 399
    Processing helix  chain 'C' and resid 411 through 416
    Processing helix  chain 'C' and resid 417 through 429
    Processing helix  chain 'C' and resid 429 through 456
      removed outlier: 4.204A  pdb=" N   GLY C 433 " --> pdb=" O   SER C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 487
      removed outlier: 4.479A  pdb=" N   TRP C 464 " --> pdb=" O   ALA C 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 494
      removed outlier: 4.083A  pdb=" N   GLU C 494 " --> pdb=" O   ASN C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 517
      removed outlier: 3.554A  pdb=" N   ARG C 498 " --> pdb=" O   GLU C 494 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE C 499 " --> pdb=" O   GLY C 495 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR C 517 " --> pdb=" O   ALA C 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 528 through 538
      removed outlier: 4.296A  pdb=" N   TYR C 532 " --> pdb=" O   GLU C 528 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU C 533 " --> pdb=" O   TRP C 529 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 539 through 547
    Processing helix  chain 'C' and resid 551 through 587
      Proline residue:  C 563  - end of helix
      Proline residue:  C 567  - end of helix
    Processing helix  chain 'C' and resid 595 through 601
      removed outlier: 4.065A  pdb=" N   PHE C 599 " --> pdb=" O   ASN C 595 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU C 600 " --> pdb=" O   LYS C 596 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR C 601 " --> pdb=" O   LYS C 597 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 595 through 601'
    Processing helix  chain 'C' and resid 601 through 607
      removed outlier: 3.645A  pdb=" N   GLU C 605 " --> pdb=" O   THR C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 608 through 612
    Processing helix  chain 'C' and resid 615 through 628
    Processing helix  chain 'C' and resid 632 through 644
      removed outlier: 3.890A  pdb=" N   MET C 636 " --> pdb=" O   TRP C 632 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 646 through 659
      removed outlier: 4.129A  pdb=" N   THR C 650 " --> pdb=" O   TRP C 646 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TYR C 651 " --> pdb=" O   TRP C 647 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE C 652 " --> pdb=" O   SER C 648 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 662 through 686
    Processing helix  chain 'D' and resid 7 through 17

    769 hydrogen bonds defined for protein.
    2259 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.13

  Time building geometry restraints manager: 3.35 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: 3351
        1.34 -     1.46: 2092
        1.46 -     1.57: 5835
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 11350
  Sorted by residual:
  bond pdb=" C   LYS A  98 "
       pdb=" N   PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.23e-02 6.61e+03 1.65e+00
  bond pdb=" CG  LEU C 440 "
       pdb=" CD1 LEU C 440 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.24e+00
  bond pdb=" CB  GLU C 468 "
       pdb=" CG  GLU C 468 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" N   PHE A  57 "
       pdb=" CA  PHE A  57 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.07e+00
  bond pdb=" N   PHE C  57 "
       pdb=" CA  PHE C  57 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.04e+00
  ... (remaining 11345 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 14967
        1.43 -     2.85: 360
        2.85 -     4.28: 81
        4.28 -     5.71: 29
        5.71 -     7.13: 3
  Bond angle restraints: 15440
  Sorted by residual:
  angle pdb=" C   THR C 246 "
        pdb=" N   VAL C 247 "
        pdb=" CA  VAL C 247 "
      ideal   model   delta    sigma   weight residual
     123.16  120.08    3.08 1.06e+00 8.90e-01 8.43e+00
  angle pdb=" C   THR A 246 "
        pdb=" N   VAL A 247 "
        pdb=" CA  VAL A 247 "
      ideal   model   delta    sigma   weight residual
     123.16  120.11    3.05 1.06e+00 8.90e-01 8.29e+00
  angle pdb=" N   VAL C 286 "
        pdb=" CA  VAL C 286 "
        pdb=" C   VAL C 286 "
      ideal   model   delta    sigma   weight residual
     113.00  109.55    3.45 1.30e+00 5.92e-01 7.04e+00
  angle pdb=" N   GLN C 393 "
        pdb=" CA  GLN C 393 "
        pdb=" CB  GLN C 393 "
      ideal   model   delta    sigma   weight residual
     110.12  113.99   -3.87 1.47e+00 4.63e-01 6.93e+00
  angle pdb=" CA  LYS C 385 "
        pdb=" CB  LYS C 385 "
        pdb=" CG  LYS C 385 "
      ideal   model   delta    sigma   weight residual
     114.10  119.04   -4.94 2.00e+00 2.50e-01 6.10e+00
  ... (remaining 15435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 6027
       17.42 -    34.84: 455
       34.84 -    52.25: 70
       52.25 -    69.67: 6
       69.67 -    87.09: 8
  Dihedral angle restraints: 6566
    sinusoidal: 2570
      harmonic: 3996
  Sorted by residual:
  dihedral pdb=" CA  SER A  56 "
           pdb=" C   SER A  56 "
           pdb=" N   PHE A  57 "
           pdb=" CA  PHE A  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.15   16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  SER C  56 "
           pdb=" C   SER C  56 "
           pdb=" N   PHE C  57 "
           pdb=" CA  PHE C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.20   16.80     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  LYS C  98 "
           pdb=" C   LYS C  98 "
           pdb=" N   PRO C  99 "
           pdb=" CA  PRO C  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 6563 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1276
       0.038 -    0.077: 381
       0.077 -    0.115: 76
       0.115 -    0.153: 14
       0.153 -    0.192: 1
  Chirality restraints: 1748
  Sorted by residual:
  chirality pdb=" CA  LYS C  98 "
            pdb=" N   LYS C  98 "
            pdb=" C   LYS C  98 "
            pdb=" CB  LYS C  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  VAL C 404 "
            pdb=" N   VAL C 404 "
            pdb=" C   VAL C 404 "
            pdb=" CB  VAL C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  VAL A 404 "
            pdb=" N   VAL A 404 "
            pdb=" C   VAL A 404 "
            pdb=" CB  VAL A 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 1745 not shown)

  Planarity restraints: 1914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 651 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.69e+00
        pdb=" C   TYR C 651 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   TYR C 651 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE C 652 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 531 "   -0.008 2.00e-02 2.50e+03   1.53e-02 2.35e+00
        pdb=" C   ARG C 531 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ARG C 531 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR C 532 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 607 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.66e+00
        pdb=" C   ASP C 607 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   ASP C 607 "    0.008 2.00e-02 2.50e+03
        pdb=" N   TYR C 608 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1911 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1579
        2.75 -     3.29: 11731
        3.29 -     3.82: 18218
        3.82 -     4.36: 20059
        4.36 -     4.90: 35187
  Nonbonded interactions: 86774
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 216 "
            pdb=" O   VAL C 657 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE C 426 "
            pdb=" OG  SER C 429 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   TYR A 107 "
            pdb=" ND2 ASN A 614 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OE2 GLU C 478 "
            pdb=" NH2 ARG C 537 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   TYR C 107 "
            pdb=" ND2 ASN C 614 "
     model   vdw
     2.253 3.120
  ... (remaining 86769 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.560
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
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      :  0.004   0.037  11350  Z= 0.158
  Angle     :  0.596   7.132  15440  Z= 0.335
  Chirality :  0.038   0.192   1748
  Planarity :  0.003   0.031   1914
  Dihedral  : 12.525  87.090   3982
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.23), residues: 1318
  helix:  1.18 (0.16), residues: 972
  sheet:  None (None), residues: 0
  loop : -0.01 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 492 
 HIS   0.005   0.002   HIS C 134 
 PHE   0.019   0.001   PHE C 248 
 TYR   0.017   0.002   TYR C 256 
 ARG   0.003   0.000   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20223 (  769)
  hydrogen bonds       : angle       6.29209 ( 2259)
  covalent geometry    : bond        0.00356 (11350)
  covalent geometry    : angle       0.59645 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.203 
Fit side-chains
REVERT: A  149 THR cc_start: 0.8234 (m) cc_final: 0.7903 (p)
REVERT: A  321 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7775 (tm-30)
REVERT: A  406 SER cc_start: 0.7673 (t) cc_final: 0.6224 (t)
REVERT: A  620 MET cc_start: 0.8906 (mmm) cc_final: 0.8676 (mmt)
REVERT: A  637 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6692 (tm-30)
REVERT: C  149 THR cc_start: 0.8179 (m) cc_final: 0.7868 (p)
REVERT: C  321 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: C  406 SER cc_start: 0.7776 (t) cc_final: 0.7462 (t)
REVERT: C  629 MET cc_start: 0.8850 (mmm) cc_final: 0.8537 (mmm)
REVERT: C  637 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6847 (tm-30)
REVERT: C  641 ASP cc_start: 0.7434 (m-30) cc_final: 0.7143 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1809
  time to fit residues: 50.2796
Evaluate side-chains
  128 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 54 optimal weight:    0.3980
   chunk 105 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 121 optimal weight:    0.7980
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 521 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.089959 restraints weight = 18523.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.37
r_work: 0.2962 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  11350  Z= 0.236
  Angle     :  0.647   7.373  15440  Z= 0.343
  Chirality :  0.041   0.196   1748
  Planarity :  0.005   0.078   1914
  Dihedral  :  4.216  17.473   1468
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.07 %
    Favored  : 91.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.23), residues: 1318
  helix:  1.78 (0.16), residues: 986
  sheet:  None (None), residues: 0
  loop : -0.15 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 492 
 HIS   0.004   0.002   HIS C 134 
 PHE   0.025   0.002   PHE C 408 
 TYR   0.023   0.002   TYR C 256 
 ARG   0.003   0.001   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06392 (  769)
  hydrogen bonds       : angle       4.38254 ( 2259)
  covalent geometry    : bond        0.00564 (11350)
  covalent geometry    : angle       0.64681 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.159 
Fit side-chains
REVERT: A   52 LEU cc_start: 0.8985 (mm) cc_final: 0.8765 (mm)
REVERT: A  443 ASN cc_start: 0.9183 (t0) cc_final: 0.8978 (t0)
REVERT: A  620 MET cc_start: 0.9079 (mmm) cc_final: 0.8723 (mmt)
REVERT: C  321 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: C  406 SER cc_start: 0.7629 (t) cc_final: 0.7181 (t)
REVERT: C  443 ASN cc_start: 0.9264 (t0) cc_final: 0.9009 (t0)
REVERT: C  620 MET cc_start: 0.9011 (mmm) cc_final: 0.8672 (mmt)
REVERT: C  637 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7635 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 137
  average time/residue: 0.1820
  time to fit residues: 39.1396
Evaluate side-chains
  133 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain C residue  395 ILE
Chi-restraints excluded: chain C residue  514 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 131 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 121 optimal weight:    0.0770
   chunk 12 optimal weight:    0.1980
   chunk 114 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.4938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.126997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.096264 restraints weight = 18529.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.39
r_work: 0.3051 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11350  Z= 0.119
  Angle     :  0.532   7.137  15440  Z= 0.276
  Chirality :  0.037   0.182   1748
  Planarity :  0.004   0.042   1914
  Dihedral  :  4.050  17.214   1468
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  9.85 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.24), residues: 1318
  helix:  2.14 (0.16), residues: 990
  sheet:  None (None), residues: 0
  loop :  0.32 (0.39), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 492 
 HIS   0.003   0.001   HIS C 416 
 PHE   0.024   0.001   PHE C 515 
 TYR   0.015   0.001   TYR C 415 
 ARG   0.007   0.000   ARG C 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04564 (  769)
  hydrogen bonds       : angle       3.90185 ( 2259)
  covalent geometry    : bond        0.00245 (11350)
  covalent geometry    : angle       0.53184 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: A  443 ASN cc_start: 0.9144 (t0) cc_final: 0.8789 (t0)
REVERT: C  287 LEU cc_start: 0.9098 (tp) cc_final: 0.8888 (mt)
REVERT: C  321 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: C  515 PHE cc_start: 0.7336 (t80) cc_final: 0.7070 (t80)
REVERT: C  564 SER cc_start: 0.9182 (t) cc_final: 0.8784 (p)
REVERT: C  637 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7819 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 152
  average time/residue: 0.1806
  time to fit residues: 42.8923
Evaluate side-chains
  127 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  272 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 100 optimal weight:    0.0370
   chunk 38 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 82 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
C 585 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.095340 restraints weight = 18241.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.37
r_work: 0.3044 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11350  Z= 0.125
  Angle     :  0.536   8.178  15440  Z= 0.277
  Chirality :  0.037   0.166   1748
  Planarity :  0.004   0.042   1914
  Dihedral  :  3.912  15.769   1468
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.54 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.24), residues: 1318
  helix:  2.09 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -0.17 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 492 
 HIS   0.002   0.001   HIS C 416 
 PHE   0.022   0.001   PHE A 368 
 TYR   0.016   0.002   TYR A 415 
 ARG   0.002   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  769)
  hydrogen bonds       : angle       3.82490 ( 2259)
  covalent geometry    : bond        0.00278 (11350)
  covalent geometry    : angle       0.53578 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: A  351 PHE cc_start: 0.8290 (t80) cc_final: 0.8076 (t80)
REVERT: A  402 GLU cc_start: 0.8649 (tp30) cc_final: 0.8356 (tp30)
REVERT: A  443 ASN cc_start: 0.9186 (t0) cc_final: 0.8924 (t0)
REVERT: A  566 MET cc_start: 0.8454 (tpp) cc_final: 0.8237 (mmm)
REVERT: C  287 LEU cc_start: 0.9102 (tp) cc_final: 0.8866 (mt)
REVERT: C  321 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7785 (tm-30)
REVERT: C  564 SER cc_start: 0.9209 (t) cc_final: 0.8805 (p)
REVERT: C  637 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7491 (tm-30)
  outliers start: 16
  outliers final: 15
  residues processed: 145
  average time/residue: 0.1968
  time to fit residues: 43.6735
Evaluate side-chains
  131 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  393 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain C residue  474 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 118 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.093291 restraints weight = 18274.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.37
r_work: 0.2989 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  11350  Z= 0.153
  Angle     :  0.554   8.832  15440  Z= 0.286
  Chirality :  0.038   0.166   1748
  Planarity :  0.004   0.045   1914
  Dihedral  :  3.931  16.328   1468
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.55 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.24), residues: 1318
  helix:  2.05 (0.16), residues: 1016
  sheet:  None (None), residues: 0
  loop : -0.23 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 492 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.022   0.001   PHE A 368 
 TYR   0.021   0.002   TYR A 415 
 ARG   0.008   0.000   ARG C 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04731 (  769)
  hydrogen bonds       : angle       3.88727 ( 2259)
  covalent geometry    : bond        0.00359 (11350)
  covalent geometry    : angle       0.55422 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: A  351 PHE cc_start: 0.8265 (t80) cc_final: 0.8028 (t80)
REVERT: A  443 ASN cc_start: 0.9211 (t0) cc_final: 0.8985 (t0)
REVERT: C  287 LEU cc_start: 0.9124 (tp) cc_final: 0.8883 (mt)
REVERT: C  321 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: C  637 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7518 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 150
  average time/residue: 0.1902
  time to fit residues: 43.6785
Evaluate side-chains
  139 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  393 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  470 VAL
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  636 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 3 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   chunk 129 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
C 117 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.126520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.095618 restraints weight = 18489.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.39
r_work: 0.3054 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11350  Z= 0.116
  Angle     :  0.533   9.621  15440  Z= 0.272
  Chirality :  0.037   0.156   1748
  Planarity :  0.003   0.040   1914
  Dihedral  :  3.858  15.531   1468
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.98 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.24), residues: 1318
  helix:  2.25 (0.17), residues: 996
  sheet:  None (None), residues: 0
  loop :  0.15 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 492 
 HIS   0.001   0.001   HIS A 134 
 PHE   0.021   0.001   PHE A 368 
 TYR   0.022   0.001   TYR A 415 
 ARG   0.006   0.000   ARG C 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  769)
  hydrogen bonds       : angle       3.73076 ( 2259)
  covalent geometry    : bond        0.00249 (11350)
  covalent geometry    : angle       0.53331 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.174 
Fit side-chains
REVERT: A  321 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: A  351 PHE cc_start: 0.8150 (t80) cc_final: 0.7892 (t80)
REVERT: A  363 ILE cc_start: 0.7561 (tp) cc_final: 0.6923 (tt)
REVERT: A  443 ASN cc_start: 0.9134 (t0) cc_final: 0.8781 (t0)
REVERT: A  538 MET cc_start: 0.8485 (mtm) cc_final: 0.8259 (ptp)
REVERT: C  154 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8743 (mm)
REVERT: C  287 LEU cc_start: 0.9056 (tp) cc_final: 0.8790 (mt)
REVERT: C  321 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: C  351 PHE cc_start: 0.8185 (t80) cc_final: 0.7879 (t80)
REVERT: C  626 LEU cc_start: 0.9068 (mt) cc_final: 0.8858 (mp)
REVERT: C  637 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7236 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 152
  average time/residue: 0.1973
  time to fit residues: 46.0192
Evaluate side-chains
  142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  541 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 133 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 74 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 ASN ** 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 = 0.3547 r_free = 0.3547 target = 0.121280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.090181 restraints weight = 18738.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.38
r_work: 0.2962 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11350  Z= 0.197
  Angle     :  0.605   9.389  15440  Z= 0.313
  Chirality :  0.040   0.267   1748
  Planarity :  0.004   0.036   1914
  Dihedral  :  3.971  14.439   1468
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.32 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.24), residues: 1318
  helix:  2.02 (0.17), residues: 1016
  sheet:  None (None), residues: 0
  loop : -0.35 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 271 
 HIS   0.004   0.001   HIS A 416 
 PHE   0.022   0.002   PHE A 368 
 TYR   0.034   0.002   TYR A 415 
 ARG   0.007   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05148 (  769)
  hydrogen bonds       : angle       3.96761 ( 2259)
  covalent geometry    : bond        0.00472 (11350)
  covalent geometry    : angle       0.60547 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 1.282 
Fit side-chains
REVERT: A  321 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: A  351 PHE cc_start: 0.8247 (t80) cc_final: 0.8028 (t80)
REVERT: A  443 ASN cc_start: 0.9245 (t0) cc_final: 0.9029 (t0)
REVERT: A  456 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7355 (tt0)
REVERT: C  216 TYR cc_start: 0.8727 (t80) cc_final: 0.8362 (t80)
REVERT: C  287 LEU cc_start: 0.9161 (tp) cc_final: 0.8912 (mt)
REVERT: C  321 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: C  456 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7204 (tt0)
REVERT: C  515 PHE cc_start: 0.7116 (t80) cc_final: 0.6906 (t80)
REVERT: C  620 MET cc_start: 0.9100 (mmm) cc_final: 0.8725 (mmt)
  outliers start: 18
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1915
  time to fit residues: 44.6492
Evaluate side-chains
  137 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  470 VAL
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  541 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.089946 restraints weight = 18746.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.39
r_work: 0.2941 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11350  Z= 0.194
  Angle     :  0.598   9.435  15440  Z= 0.308
  Chirality :  0.040   0.267   1748
  Planarity :  0.004   0.052   1914
  Dihedral  :  4.011  14.229   1468
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.32 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.24), residues: 1318
  helix:  2.01 (0.17), residues: 1004
  sheet:  None (None), residues: 0
  loop : -0.34 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 271 
 HIS   0.003   0.001   HIS C 134 
 PHE   0.022   0.001   PHE A 368 
 TYR   0.020   0.002   TYR C 256 
 ARG   0.011   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05079 (  769)
  hydrogen bonds       : angle       3.97953 ( 2259)
  covalent geometry    : bond        0.00464 (11350)
  covalent geometry    : angle       0.59828 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8345 (mm-30)
REVERT: A  321 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: A  351 PHE cc_start: 0.8222 (t80) cc_final: 0.7981 (t80)
REVERT: A  443 ASN cc_start: 0.9234 (t0) cc_final: 0.9012 (t0)
REVERT: A  456 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7324 (tt0)
REVERT: A  682 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7841 (tt0)
REVERT: C  287 LEU cc_start: 0.9183 (tp) cc_final: 0.8947 (mt)
REVERT: C  321 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: C  456 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7194 (tt0)
REVERT: C  620 MET cc_start: 0.9089 (mmm) cc_final: 0.8707 (mmt)
  outliers start: 18
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1801
  time to fit residues: 41.1742
Evaluate side-chains
  142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  470 VAL
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  541 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 117 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 70 optimal weight:    0.4980
   chunk 100 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 121 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:
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.125189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.094552 restraints weight = 18512.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.38
r_work: 0.3023 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11350  Z= 0.119
  Angle     :  0.550   9.916  15440  Z= 0.280
  Chirality :  0.037   0.252   1748
  Planarity :  0.004   0.053   1914
  Dihedral  :  3.898  14.879   1468
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.08 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.24), residues: 1318
  helix:  2.21 (0.17), residues: 996
  sheet:  None (None), residues: 0
  loop :  0.07 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 505 
 HIS   0.002   0.001   HIS C 134 
 PHE   0.021   0.001   PHE A 368 
 TYR   0.020   0.001   TYR A 415 
 ARG   0.011   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04175 (  769)
  hydrogen bonds       : angle       3.75893 ( 2259)
  covalent geometry    : bond        0.00252 (11350)
  covalent geometry    : angle       0.55047 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.246 
Fit side-chains
REVERT: A  142 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8338 (mm-30)
REVERT: A  321 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: A  351 PHE cc_start: 0.8013 (t80) cc_final: 0.7782 (t80)
REVERT: A  443 ASN cc_start: 0.9198 (t0) cc_final: 0.8897 (t0)
REVERT: A  456 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7296 (tt0)
REVERT: A  682 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7853 (tt0)
REVERT: C  154 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: C  287 LEU cc_start: 0.9104 (tp) cc_final: 0.8856 (mt)
REVERT: C  321 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: C  351 PHE cc_start: 0.8261 (t80) cc_final: 0.7972 (t80)
REVERT: C  456 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7281 (tt0)
REVERT: C  637 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7842 (tm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 146
  average time/residue: 0.1986
  time to fit residues: 44.8190
Evaluate side-chains
  134 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  470 VAL
Chi-restraints excluded: chain C residue  541 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 124 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.125630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.095063 restraints weight = 18342.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.37
r_work: 0.3022 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11350  Z= 0.124
  Angle     :  0.558  10.312  15440  Z= 0.283
  Chirality :  0.037   0.247   1748
  Planarity :  0.003   0.038   1914
  Dihedral  :  3.830  14.716   1468
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 16.25 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.24), residues: 1318
  helix:  2.11 (0.17), residues: 1016
  sheet:  None (None), residues: 0
  loop : -0.37 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 505 
 HIS   0.002   0.001   HIS C 134 
 PHE   0.021   0.001   PHE A 368 
 TYR   0.016   0.001   TYR C 256 
 ARG   0.010   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  769)
  hydrogen bonds       : angle       3.72909 ( 2259)
  covalent geometry    : bond        0.00275 (11350)
  covalent geometry    : angle       0.55772 (15440)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.185 
Fit side-chains
REVERT: A  142 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8343 (mm-30)
REVERT: A  321 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: A  351 PHE cc_start: 0.7982 (t80) cc_final: 0.7764 (t80)
REVERT: A  443 ASN cc_start: 0.9187 (t0) cc_final: 0.8943 (t0)
REVERT: A  456 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7270 (tt0)
REVERT: A  682 GLU cc_start: 0.8613 (mm-30) cc_final: 0.7947 (tt0)
REVERT: C  154 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8773 (mm)
REVERT: C  287 LEU cc_start: 0.9089 (tp) cc_final: 0.8828 (mt)
REVERT: C  321 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: C  351 PHE cc_start: 0.8243 (t80) cc_final: 0.7951 (t80)
REVERT: C  637 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7859 (tm-30)
  outliers start: 14
  outliers final: 13
  residues processed: 145
  average time/residue: 0.1887
  time to fit residues: 42.2297
Evaluate side-chains
  138 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  470 VAL
Chi-restraints excluded: chain C residue  541 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 618 ASN ** 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 = 0.3562 r_free = 0.3562 target = 0.122580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.091888 restraints weight = 18530.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.37
r_work: 0.2978 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11350  Z= 0.169
  Angle     :  0.592   9.934  15440  Z= 0.302
  Chirality :  0.039   0.254   1748
  Planarity :  0.004   0.043   1914
  Dihedral  :  3.892  14.509   1468
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.25 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.24), residues: 1318
  helix:  2.08 (0.17), residues: 1006
  sheet:  None (None), residues: 0
  loop : -0.42 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 271 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.022   0.001   PHE A 368 
 TYR   0.019   0.002   TYR C 256 
 ARG   0.010   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  769)
  hydrogen bonds       : angle       3.87906 ( 2259)
  covalent geometry    : bond        0.00400 (11350)
  covalent geometry    : angle       0.59181 (15440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5260.68 seconds
wall clock time: 90 minutes 46.72 seconds (5446.72 seconds total)