Starting phenix.real_space_refine
on Tue Apr 29 18:22:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zvq_60512/04_2025/8zvq_60512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zvq_60512/04_2025/8zvq_60512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zvq_60512/04_2025/8zvq_60512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zvq_60512/04_2025/8zvq_60512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zvq_60512/04_2025/8zvq_60512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zvq_60512/04_2025/8zvq_60512.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.145
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5684      2.51       5
     N    1560      2.21       5
     O    1602      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8896
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4448
          Classifications: {'peptide': 576}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 534}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4448
          Classifications: {'peptide': 576}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 534}
          Chain breaks: 3
  Time building chain proxies: 5.72, per 1000 atoms: 0.64
  Number of scatterers: 8896
  At special positions: 0
  Unit cell: (113.048, 114.135, 66.307, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1602      8.00
     N    1560      7.00
     C    5684      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: 2.41
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      52.4% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 23
      removed outlier: 3.916A  pdb=" N   LEU A  10 " --> pdb=" O   MET A   6 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A  11 " --> pdb=" O   THR A   7 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A  13 " --> pdb=" O   SER A   9 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A  14 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   GLU A  15 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   ASP A  16 " --> pdb=" O   THR A  12 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASN A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A  21 " --> pdb=" O   ASN A  17 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 61
      Proline residue:  A  49  - end of helix
    Processing helix  chain 'A' and resid 71 through 96
    Processing helix  chain 'A' and resid 104 through 134
    Processing helix  chain 'A' and resid 146 through 158
    Processing helix  chain 'A' and resid 162 through 165
      No H-bonds generated for 'chain 'A' and resid 162 through 165'
    Processing helix  chain 'A' and resid 175 through 197
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 219 through 232
      removed outlier: 4.366A  pdb=" N   GLY A 223 " --> pdb=" O   PRO A 219 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ALA A 224 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLU A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ARG A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   THR A 230 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 246
      removed outlier: 4.385A  pdb=" N   ALA A 240 " --> pdb=" O   HIS A 236 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   PHE A 241 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TRP A 242 " --> pdb=" O   TRP A 238 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ASN A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   THR A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   GLU A 246 " --> pdb=" O   TRP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 256
      removed outlier: 3.889A  pdb=" N   SER A 252 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ASN A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   MET A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 321
      removed outlier: 4.909A  pdb=" N   LEU A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 373
      removed outlier: 4.837A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      Proline residue:  A 364  - end of helix
      removed outlier: 4.410A  pdb=" N   SER A 368 " --> pdb=" O   PRO A 364 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN A 371 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   GLU A 372 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 406
      removed outlier: 3.623A  pdb=" N   GLU A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   CYS A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ILE A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   LYS A 406 " --> pdb=" O   CYS A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 439
      removed outlier: 6.332A  pdb=" N   ASN A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   LEU A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS A 430 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 434 " --> pdb=" O   CYS A 430 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 469
      removed outlier: 3.660A  pdb=" N   LEU A 467 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER A 468 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU A 469 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 464 through 469'
    Processing helix  chain 'A' and resid 476 through 486
      removed outlier: 3.752A  pdb=" N   VAL A 483 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   SER A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 665
      removed outlier: 3.942A  pdb=" N   LYS A 665 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 662 through 665'
    Processing helix  chain 'A' and resid 671 through 673
      No H-bonds generated for 'chain 'A' and resid 671 through 673'
    Processing helix  chain 'A' and resid 676 through 681
      removed outlier: 4.027A  pdb=" N   LYS A 680 " --> pdb=" O   ASP A 676 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   SER A 681 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 676 through 681'
    Processing helix  chain 'A' and resid 696 through 708
      removed outlier: 3.699A  pdb=" N   LEU A 702 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA A 703 " --> pdb=" O   SER A 699 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG A 704 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASN A 708 " --> pdb=" O   ARG A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 728
    Processing helix  chain 'A' and resid 733 through 750
      removed outlier: 3.657A  pdb=" N   LEU A 741 " --> pdb=" O   GLN A 737 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   CYS A 742 " --> pdb=" O   ALA A 738 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   VAL A 743 " --> pdb=" O   ALA A 739 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 744 " --> pdb=" O   GLU A 740 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ARG A 745 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A 747 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LEU A 748 " --> pdb=" O   GLU A 744 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   VAL A 749 " --> pdb=" O   ARG A 745 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   LEU A 750 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 23
      removed outlier: 4.138A  pdb=" N   LEU B  10 " --> pdb=" O   MET B   6 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL B  11 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LEU B  13 " --> pdb=" O   SER B   9 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   ALA B  14 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLU B  15 " --> pdb=" O   VAL B  11 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   ASP B  16 " --> pdb=" O   THR B  12 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ASN B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE B  21 " --> pdb=" O   ASN B  17 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER B  23 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 61
      Proline residue:  B  49  - end of helix
    Processing helix  chain 'B' and resid 71 through 96
    Processing helix  chain 'B' and resid 104 through 134
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 162 through 165
      No H-bonds generated for 'chain 'B' and resid 162 through 165'
    Processing helix  chain 'B' and resid 175 through 197
      Proline residue:  B 179  - end of helix
    Processing helix  chain 'B' and resid 219 through 232
      removed outlier: 4.209A  pdb=" N   GLY B 223 " --> pdb=" O   PRO B 219 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   ALA B 224 " --> pdb=" O   GLU B 220 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   ARG B 228 " --> pdb=" O   ALA B 224 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLN B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 246
      removed outlier: 4.091A  pdb=" N   ALA B 240 " --> pdb=" O   HIS B 236 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   TRP B 242 " --> pdb=" O   TRP B 238 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASN B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   THR B 245 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   GLU B 246 " --> pdb=" O   TRP B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 256
      removed outlier: 4.253A  pdb=" N   MET B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 321
      removed outlier: 4.527A  pdb=" N   LEU B 321 " --> pdb=" O   GLU B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 373
      removed outlier: 4.706A  pdb=" N   GLU B 363 " --> pdb=" O   SER B 359 " (cutoff:3.500A)
      Proline residue:  B 364  - end of helix
      removed outlier: 4.518A  pdb=" N   SER B 368 " --> pdb=" O   PRO B 364 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN B 371 " --> pdb=" O   LYS B 367 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLU B 372 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 406
      removed outlier: 3.695A  pdb=" N   GLU B 396 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   CYS B 397 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LYS B 406 " --> pdb=" O   CYS B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 439
      removed outlier: 5.532A  pdb=" N   ASN B 428 " --> pdb=" O   SER B 424 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   LEU B 429 " --> pdb=" O   ALA B 425 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   CYS B 430 " --> pdb=" O   GLY B 426 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   PHE B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   ALA B 434 " --> pdb=" O   CYS B 430 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 435 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA B 437 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ALA B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 469
      removed outlier: 3.713A  pdb=" N   LEU B 467 " --> pdb=" O   SER B 464 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER B 468 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU B 469 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 464 through 469'
    Processing helix  chain 'B' and resid 476 through 486
      removed outlier: 4.304A  pdb=" N   LYS B 481 " --> pdb=" O   SER B 477 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   SER B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA B 485 " --> pdb=" O   LYS B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 665
    Processing helix  chain 'B' and resid 671 through 673
      No H-bonds generated for 'chain 'B' and resid 671 through 673'
    Processing helix  chain 'B' and resid 676 through 681
      removed outlier: 3.887A  pdb=" N   LYS B 680 " --> pdb=" O   ASP B 676 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   SER B 681 " --> pdb=" O   SER B 677 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 676 through 681'
    Processing helix  chain 'B' and resid 696 through 708
      removed outlier: 3.553A  pdb=" N   ALA B 703 " --> pdb=" O   SER B 699 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASN B 708 " --> pdb=" O   ARG B 704 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 728
    Processing helix  chain 'B' and resid 733 through 750
      removed outlier: 4.849A  pdb=" N   GLN B 737 " --> pdb=" O   ARG B 733 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA B 738 " --> pdb=" O   GLU B 734 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   CYS B 742 " --> pdb=" O   ALA B 738 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL B 743 " --> pdb=" O   ALA B 739 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LEU B 748 " --> pdb=" O   GLU B 744 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   VAL B 749 " --> pdb=" O   ARG B 745 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU B 750 " --> pdb=" O   ILE B 746 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'A' and resid 263 through 269
      removed outlier: 3.739A  pdb=" N   VAL A 263 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A 302 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL A 300 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 274 through 277
      removed outlier: 5.049A  pdb=" N   PHE A 274 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   ILE A 288 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   MET A 276 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
    Processing sheet with id=C, first strand: chain 'A' and resid 376 through 380
      removed outlier: 3.555A  pdb=" N   ILE A 346 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ARG A 417 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   VAL A 347 " --> pdb=" O   ARG A 417 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   CYS A 419 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   PHE A 349 " --> pdb=" O   CYS A 419 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ALA A 421 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   GLY A 447 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 8.389A  pdb=" N   GLY A 422 " --> pdb=" O   GLY A 447 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   MET A 449 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'A' and resid 685 through 690
    Processing sheet with id=E, first strand: chain 'B' and resid 263 through 269
      removed outlier: 3.750A  pdb=" N   VAL B 263 " --> pdb=" O   SER B 306 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   VAL B 302 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 269 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL B 300 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
    Processing sheet with id=F, first strand: chain 'B' and resid 274 through 277
      removed outlier: 4.785A  pdb=" N   PHE B 274 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
    Processing sheet with id=G, first strand: chain 'B' and resid 376 through 380
      removed outlier: 6.192A  pdb=" N   ARG B 417 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   VAL B 347 " --> pdb=" O   ARG B 417 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   CYS B 419 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   PHE B 349 " --> pdb=" O   CYS B 419 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ALA B 421 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   GLY B 447 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
      removed outlier: 8.716A  pdb=" N   GLY B 422 " --> pdb=" O   GLY B 447 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   MET B 449 " --> pdb=" O   GLY B 422 " (cutoff:3.500A)
    Processing sheet with id=H, first strand: chain 'B' and resid 685 through 690

    330 hydrogen bonds defined for protein.
    981 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: 3.15

  Time building geometry restraints manager: 2.82 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: 2848
        1.34 -     1.46: 1662
        1.46 -     1.58: 4522
        1.58 -     1.70: 2
        1.70 -     1.82: 74
  Bond restraints: 9108
  Sorted by residual:
  bond pdb=" N   PRO A 752 "
       pdb=" CD  PRO A 752 "
    ideal  model  delta    sigma   weight residual
    1.473  1.421  0.052 1.40e-02 5.10e+03 1.35e+01
  bond pdb=" SD  MET B 678 "
       pdb=" CE  MET B 678 "
    ideal  model  delta    sigma   weight residual
    1.791  1.734  0.057 2.50e-02 1.60e+03 5.29e+00
  bond pdb=" C   GLU B 275 "
       pdb=" N   MET B 276 "
    ideal  model  delta    sigma   weight residual
    1.325  1.354 -0.029 1.25e-02 6.40e+03 5.27e+00
  bond pdb=" CB  PRO A 340 "
       pdb=" CG  PRO A 340 "
    ideal  model  delta    sigma   weight residual
    1.492  1.596 -0.104 5.00e-02 4.00e+02 4.31e+00
  bond pdb=" SD  MET A 456 "
       pdb=" CE  MET A 456 "
    ideal  model  delta    sigma   weight residual
    1.791  1.740  0.051 2.50e-02 1.60e+03 4.09e+00
  ... (remaining 9103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.10: 12260
        4.10 -     8.21: 104
        8.21 -    12.31: 14
       12.31 -    16.41: 4
       16.41 -    20.51: 2
  Bond angle restraints: 12384
  Sorted by residual:
  angle pdb=" N   PRO A 752 "
        pdb=" CD  PRO A 752 "
        pdb=" CG  PRO A 752 "
      ideal   model   delta    sigma   weight residual
     103.20   92.85   10.35 1.50e+00 4.44e-01 4.76e+01
  angle pdb=" CA  LEU B 728 "
        pdb=" CB  LEU B 728 "
        pdb=" CG  LEU B 728 "
      ideal   model   delta    sigma   weight residual
     116.30  136.81  -20.51 3.50e+00 8.16e-02 3.44e+01
  angle pdb=" CA  PRO A 340 "
        pdb=" N   PRO A 340 "
        pdb=" CD  PRO A 340 "
      ideal   model   delta    sigma   weight residual
     112.00  104.27    7.73 1.40e+00 5.10e-01 3.05e+01
  angle pdb=" CA  PRO A 752 "
        pdb=" N   PRO A 752 "
        pdb=" CD  PRO A 752 "
      ideal   model   delta    sigma   weight residual
     112.00  104.31    7.69 1.40e+00 5.10e-01 3.01e+01
  angle pdb=" CA  PRO A 752 "
        pdb=" CB  PRO A 752 "
        pdb=" CG  PRO A 752 "
      ideal   model   delta    sigma   weight residual
     104.50   94.55    9.95 1.90e+00 2.77e-01 2.74e+01
  ... (remaining 12379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4627
       17.94 -    35.88: 642
       35.88 -    53.82: 199
       53.82 -    71.76: 21
       71.76 -    89.69: 13
  Dihedral angle restraints: 5502
    sinusoidal: 2166
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CA  MET A 247 "
           pdb=" C   MET A 247 "
           pdb=" N   GLU A 248 "
           pdb=" CA  GLU A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.37  -24.63     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  ILE B 288 "
           pdb=" C   ILE B 288 "
           pdb=" N   SER B 289 "
           pdb=" CA  SER B 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.55   21.45     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  MET B 276 "
           pdb=" C   MET B 276 "
           pdb=" N   PRO B 277 "
           pdb=" CA  PRO B 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.19   18.81     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 5499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1228
       0.073 -    0.146: 160
       0.146 -    0.220: 21
       0.220 -    0.293: 2
       0.293 -    0.366: 1
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" CB  ILE B 177 "
            pdb=" CA  ILE B 177 "
            pdb=" CG1 ILE B 177 "
            pdb=" CG2 ILE B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CG  LEU A 474 "
            pdb=" CB  LEU A 474 "
            pdb=" CD1 LEU A 474 "
            pdb=" CD2 LEU A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  ILE A 100 "
            pdb=" CA  ILE A 100 "
            pdb=" CG1 ILE A 100 "
            pdb=" CG2 ILE A 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1409 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 339 "    0.070 5.00e-02 4.00e+02   1.02e-01 1.66e+01
        pdb=" N   PRO A 340 "   -0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A 340 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 340 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 417 "    0.290 9.50e-02 1.11e+02   1.30e-01 1.07e+01
        pdb=" NE  ARG A 417 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 417 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 417 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 417 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 674 "    0.050 5.00e-02 4.00e+02   7.63e-02 9.32e+00
        pdb=" N   PRO B 675 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 675 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 675 "    0.041 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.21: 8
        2.21 -     2.88: 3372
        2.88 -     3.55: 12473
        3.55 -     4.23: 19707
        4.23 -     4.90: 33512
  Nonbonded interactions: 69072
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 178 "
            pdb=" NE2 GLN A 182 "
     model   vdw
     1.532 3.120
  nonbonded pdb=" NH1 ARG A 262 "
            pdb=" O   TYR A 307 "
     model   vdw
     1.605 3.120
  nonbonded pdb=" O   ARG A 178 "
            pdb=" CD  GLN A 182 "
     model   vdw
     1.701 3.270
  nonbonded pdb=" CA  PRO A 179 "
            pdb=" OE1 GLN A 182 "
     model   vdw
     1.780 3.470
  nonbonded pdb=" C   ARG A 178 "
            pdb=" NE2 GLN A 182 "
     model   vdw
     1.808 3.350
  ... (remaining 69067 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 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.09 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:             3.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.120
  Find NCS groups from input model:        0.310
  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:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5764
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104   9108  Z= 0.222
  Angle     :  1.030  20.515  12384  Z= 0.493
  Chirality :  0.052   0.366   1412
  Planarity :  0.009   0.130   1604
  Dihedral  : 18.071  89.694   3342
  Min Nonbonded Distance : 1.532

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 31.87 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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 (0.23), residues: 1136
  helix: -1.12 (0.22), residues: 480
  sheet: -1.04 (0.53), residues: 94
  loop : -1.89 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 369 
 HIS   0.017   0.002   HIS B 160 
 PHE   0.052   0.003   PHE B 180 
 TYR   0.023   0.002   TYR A 195 
 ARG   0.009   0.001   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17850 (  330)
  hydrogen bonds       : angle       6.69379 (  981)
  covalent geometry    : bond        0.00510 ( 9108)
  covalent geometry    : angle       1.02980 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 97
  average time/residue: 0.2381
  time to fit residues: 31.8149
Evaluate side-chains
  95 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue  256 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 350 HIS
A 686 HIS
A 711 GLN
B   8 GLN
B  31 GLN
B  77 HIS
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 HIS
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 458 GLN
** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.250235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.215402 restraints weight = 9611.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 3.18
r_work: 0.4352 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4377 r_free = 0.4377    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4375 r_free = 0.4375    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5874
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9108  Z= 0.168
  Angle     :  0.702  14.481  12384  Z= 0.339
  Chirality :  0.044   0.165   1412
  Planarity :  0.006   0.062   1604
  Dihedral  :  4.928  35.215   1265
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 28.83 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -1.63 (0.24), residues: 1136
  helix: -0.33 (0.23), residues: 474
  sheet: -1.03 (0.53), residues: 94
  loop : -1.74 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 403 
 HIS   0.007   0.001   HIS B 160 
 PHE   0.023   0.002   PHE B 180 
 TYR   0.019   0.002   TYR B 452 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04896 (  330)
  hydrogen bonds       : angle       4.69402 (  981)
  covalent geometry    : bond        0.00397 ( 9108)
  covalent geometry    : angle       0.70178 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 106
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  420 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6987 (mt)
REVERT: A  672 LEU cc_start: 0.3785 (OUTLIER) cc_final: 0.3186 (mm)
REVERT: A  744 GLU cc_start: 0.5158 (OUTLIER) cc_final: 0.4075 (mp0)
REVERT: B  182 GLN cc_start: 0.7183 (mt0) cc_final: 0.6818 (mt0)
REVERT: B  303 ARG cc_start: 0.7409 (ptm-80) cc_final: 0.7131 (ptm160)
REVERT: B  479 LEU cc_start: 0.7044 (pp) cc_final: 0.6473 (mp)
  outliers start: 46
  outliers final: 19
  residues processed: 140
  average time/residue: 0.2194
  time to fit residues: 42.6173
Evaluate side-chains
  117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  693 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 110 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 428 ASN
B  70 ASN
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 723 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.252731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.219843 restraints weight = 9896.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.4594 rms_B_bonded: 2.63
r_work: 0.4395 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4419 r_free = 0.4419    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4418 r_free = 0.4418    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5816
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9108  Z= 0.135
  Angle     :  0.663  13.215  12384  Z= 0.313
  Chirality :  0.043   0.173   1412
  Planarity :  0.005   0.054   1604
  Dihedral  :  4.550  18.563   1262
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 30.40 %
    Favored  : 64.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -1.31 (0.25), residues: 1136
  helix:  0.02 (0.24), residues: 488
  sheet: -1.03 (0.50), residues: 108
  loop : -1.66 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 403 
 HIS   0.006   0.001   HIS B 160 
 PHE   0.027   0.001   PHE B 644 
 TYR   0.028   0.001   TYR A 156 
 ARG   0.003   0.000   ARG B 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  330)
  hydrogen bonds       : angle       4.36784 (  981)
  covalent geometry    : bond        0.00318 ( 9108)
  covalent geometry    : angle       0.66272 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 96
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 LEU cc_start: 0.3655 (OUTLIER) cc_final: 0.3341 (tt)
REVERT: A  182 GLN cc_start: 0.6825 (mp10) cc_final: 0.6572 (mp10)
REVERT: A  225 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5851 (mp0)
REVERT: A  367 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7655 (mtpp)
REVERT: A  378 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7966 (tt)
REVERT: A  672 LEU cc_start: 0.4093 (OUTLIER) cc_final: 0.3218 (mm)
REVERT: A  744 GLU cc_start: 0.5097 (OUTLIER) cc_final: 0.4044 (mp0)
REVERT: B  303 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.7098 (ptm160)
REVERT: B  377 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7732 (mp)
REVERT: B  479 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6265 (mp)
  outliers start: 48
  outliers final: 29
  residues processed: 133
  average time/residue: 0.2138
  time to fit residues: 39.7131
Evaluate side-chains
  131 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  693 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    0.0270
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0040
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.2828

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 723 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.256310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.221355 restraints weight = 9727.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.4601 rms_B_bonded: 2.88
r_work: 0.4419 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4442 r_free = 0.4442    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4441 r_free = 0.4441    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5665
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9108  Z= 0.101
  Angle     :  0.594  13.879  12384  Z= 0.277
  Chirality :  0.040   0.174   1412
  Planarity :  0.005   0.050   1604
  Dihedral  :  4.192  18.744   1262
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 29.98 %
    Favored  : 64.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.89 (0.25), residues: 1136
  helix:  0.45 (0.24), residues: 490
  sheet: -0.96 (0.49), residues: 108
  loop : -1.48 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 369 
 HIS   0.006   0.001   HIS B 160 
 PHE   0.008   0.001   PHE B 164 
 TYR   0.015   0.001   TYR A 156 
 ARG   0.003   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03421 (  330)
  hydrogen bonds       : angle       4.05521 (  981)
  covalent geometry    : bond        0.00236 ( 9108)
  covalent geometry    : angle       0.59391 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 101
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.3065 (tt)
REVERT: A  171 PHE cc_start: 0.7271 (p90) cc_final: 0.7049 (p90)
REVERT: A  367 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7817 (mtpp)
REVERT: A  420 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6942 (mt)
REVERT: A  672 LEU cc_start: 0.3841 (OUTLIER) cc_final: 0.3207 (mm)
REVERT: B  377 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7673 (mp)
REVERT: B  420 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6386 (tt)
REVERT: B  479 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.5925 (mt)
  outliers start: 56
  outliers final: 26
  residues processed: 143
  average time/residue: 0.1865
  time to fit residues: 38.1006
Evaluate side-chains
  125 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  693 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 63 optimal weight:    0.4980
   chunk 102 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 348 HIS
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.253573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.220640 restraints weight = 9718.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.4586 rms_B_bonded: 2.68
r_work: 0.4394 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.4394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4425
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4425 r_free = 0.4425    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4425 r_free = 0.4425    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.4425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5813
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9108  Z= 0.124
  Angle     :  0.647  15.845  12384  Z= 0.298
  Chirality :  0.042   0.222   1412
  Planarity :  0.005   0.050   1604
  Dihedral  :  4.178  18.984   1262
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 29.25 %
    Favored  : 64.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.80 (0.25), residues: 1136
  helix:  0.51 (0.24), residues: 492
  sheet: -0.97 (0.50), residues: 108
  loop : -1.41 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 369 
 HIS   0.005   0.001   HIS B 160 
 PHE   0.015   0.001   PHE B 237 
 TYR   0.015   0.001   TYR A 156 
 ARG   0.003   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03852 (  330)
  hydrogen bonds       : angle       4.07242 (  981)
  covalent geometry    : bond        0.00297 ( 9108)
  covalent geometry    : angle       0.64655 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 99
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.5981 (m-80)
REVERT: A   87 LEU cc_start: 0.3813 (OUTLIER) cc_final: 0.3507 (tt)
REVERT: A  171 PHE cc_start: 0.7332 (p90) cc_final: 0.7058 (p90)
REVERT: A  225 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5721 (mp0)
REVERT: A  303 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7444 (ptm160)
REVERT: A  420 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7036 (mt)
REVERT: A  672 LEU cc_start: 0.4278 (OUTLIER) cc_final: 0.3507 (mm)
REVERT: A  744 GLU cc_start: 0.4736 (OUTLIER) cc_final: 0.3917 (mp0)
REVERT: B   66 GLU cc_start: 0.7013 (mp0) cc_final: 0.6807 (mt-10)
REVERT: B  377 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: B  479 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6432 (mt)
  outliers start: 60
  outliers final: 37
  residues processed: 146
  average time/residue: 0.2111
  time to fit residues: 42.5336
Evaluate side-chains
  140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 94
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  693 ASP
Chi-restraints excluded: chain B residue  723 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.249302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.214201 restraints weight = 9789.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.4542 rms_B_bonded: 2.81
r_work: 0.4349 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4376 r_free = 0.4376    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4376 r_free = 0.4376    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.4376
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9108  Z= 0.139
  Angle     :  0.666  15.457  12384  Z= 0.311
  Chirality :  0.043   0.203   1412
  Planarity :  0.005   0.050   1604
  Dihedral  :  4.243  17.680   1262
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 29.66 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.85 (0.26), residues: 1136
  helix:  0.44 (0.24), residues: 490
  sheet: -1.08 (0.50), residues: 110
  loop : -1.38 (0.28), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 369 
 HIS   0.004   0.001   HIS B 160 
 PHE   0.012   0.001   PHE B 237 
 TYR   0.016   0.002   TYR A 452 
 ARG   0.003   0.000   ARG B 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  330)
  hydrogen bonds       : angle       4.20758 (  981)
  covalent geometry    : bond        0.00332 ( 9108)
  covalent geometry    : angle       0.66626 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 102
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6281 (t80)
REVERT: A   87 LEU cc_start: 0.3673 (OUTLIER) cc_final: 0.3363 (tt)
REVERT: A  171 PHE cc_start: 0.7391 (p90) cc_final: 0.7028 (p90)
REVERT: A  182 GLN cc_start: 0.7007 (mp10) cc_final: 0.6654 (mp10)
REVERT: A  225 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5778 (mt-10)
REVERT: A  420 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7272 (mt)
REVERT: A  672 LEU cc_start: 0.4161 (OUTLIER) cc_final: 0.3194 (mm)
REVERT: A  736 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6172 (ttm-80)
REVERT: A  744 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.3944 (mp0)
REVERT: B   66 GLU cc_start: 0.7080 (mp0) cc_final: 0.6868 (mt-10)
REVERT: B  303 ARG cc_start: 0.7522 (ptm-80) cc_final: 0.7135 (ptm160)
REVERT: B  377 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7720 (mp)
REVERT: B  479 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6430 (mt)
  outliers start: 65
  outliers final: 45
  residues processed: 153
  average time/residue: 0.2431
  time to fit residues: 51.7350
Evaluate side-chains
  151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 97
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  690 CYS
Chi-restraints excluded: chain B residue  693 ASP
Chi-restraints excluded: chain B residue  723 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0050
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 30 optimal weight:    0.2980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 723 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.253063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.218300 restraints weight = 9737.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4575 rms_B_bonded: 2.80
r_work: 0.4388 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4418 r_free = 0.4418    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4418 r_free = 0.4418    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.4418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5786
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9108  Z= 0.111
  Angle     :  0.651  14.597  12384  Z= 0.299
  Chirality :  0.042   0.176   1412
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.091  19.001   1262
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 30.29 %
    Favored  : 63.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.68 (0.26), residues: 1136
  helix:  0.64 (0.24), residues: 488
  sheet: -0.97 (0.51), residues: 110
  loop : -1.36 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 369 
 HIS   0.005   0.001   HIS B 160 
 PHE   0.008   0.001   PHE A  37 
 TYR   0.015   0.001   TYR A 156 
 ARG   0.003   0.000   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  330)
  hydrogen bonds       : angle       4.10515 (  981)
  covalent geometry    : bond        0.00262 ( 9108)
  covalent geometry    : angle       0.65106 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 96
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.5969 (m-80)
REVERT: A   87 LEU cc_start: 0.3661 (OUTLIER) cc_final: 0.3352 (tt)
REVERT: A  171 PHE cc_start: 0.7272 (p90) cc_final: 0.6933 (p90)
REVERT: A  182 GLN cc_start: 0.7053 (mp10) cc_final: 0.6689 (mp10)
REVERT: A  303 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7263 (ptm160)
REVERT: A  420 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7131 (mt)
REVERT: A  736 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6204 (ttm-80)
REVERT: A  744 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.3898 (mp0)
REVERT: B  377 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7624 (mp)
REVERT: B  479 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6371 (mt)
REVERT: B  672 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4371 (mm)
  outliers start: 58
  outliers final: 37
  residues processed: 144
  average time/residue: 0.2161
  time to fit residues: 42.8148
Evaluate side-chains
  141 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 95
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  672 LEU
Chi-restraints excluded: chain B residue  690 CYS
Chi-restraints excluded: chain B residue  693 ASP
Chi-restraints excluded: chain B residue  723 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.0970
   chunk 102 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN
** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 711 GLN
B 723 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.250468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.215206 restraints weight = 9910.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4546 rms_B_bonded: 2.83
r_work: 0.4357 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4390 r_free = 0.4390    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4390 r_free = 0.4390    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.4390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5845
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9108  Z= 0.130
  Angle     :  0.678  14.573  12384  Z= 0.312
  Chirality :  0.043   0.174   1412
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.145  18.560   1262
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 30.08 %
    Favored  : 63.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.68 (0.26), residues: 1136
  helix:  0.63 (0.24), residues: 488
  sheet: -0.99 (0.51), residues: 110
  loop : -1.33 (0.28), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 403 
 HIS   0.016   0.001   HIS B 723 
 PHE   0.008   0.001   PHE A  37 
 TYR   0.015   0.001   TYR B 156 
 ARG   0.003   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  330)
  hydrogen bonds       : angle       4.17490 (  981)
  covalent geometry    : bond        0.00310 ( 9108)
  covalent geometry    : angle       0.67762 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 99
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.5968 (m-80)
REVERT: A   87 LEU cc_start: 0.3590 (OUTLIER) cc_final: 0.3283 (tt)
REVERT: A  171 PHE cc_start: 0.7021 (p90) cc_final: 0.6641 (p90)
REVERT: A  225 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5721 (mt-10)
REVERT: A  303 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7406 (ptm160)
REVERT: A  420 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7282 (mt)
REVERT: A  736 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6217 (ttm-80)
REVERT: A  744 GLU cc_start: 0.4887 (OUTLIER) cc_final: 0.3994 (mp0)
REVERT: B  377 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7646 (mp)
REVERT: B  479 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6565 (mt)
REVERT: B  672 LEU cc_start: 0.4655 (OUTLIER) cc_final: 0.4070 (mm)
  outliers start: 57
  outliers final: 39
  residues processed: 147
  average time/residue: 0.2269
  time to fit residues: 45.5996
Evaluate side-chains
  143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 94
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  672 LEU
Chi-restraints excluded: chain B residue  690 CYS
Chi-restraints excluded: chain B residue  723 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    0.0770
   chunk 27 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 104 optimal weight:    0.1980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.254917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.220369 restraints weight = 9750.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.4591 rms_B_bonded: 2.78
r_work: 0.4392 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4414 r_free = 0.4414    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4414 r_free = 0.4414    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.4414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9108  Z= 0.112
  Angle     :  0.665  14.051  12384  Z= 0.312
  Chirality :  0.042   0.207   1412
  Planarity :  0.004   0.048   1604
  Dihedral  :  4.042  18.210   1262
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 30.82 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.55 (0.26), residues: 1136
  helix:  0.75 (0.24), residues: 486
  sheet: -0.84 (0.51), residues: 110
  loop : -1.29 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 403 
 HIS   0.012   0.001   HIS B 723 
 PHE   0.007   0.001   PHE A  37 
 TYR   0.015   0.001   TYR B 156 
 ARG   0.004   0.000   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03695 (  330)
  hydrogen bonds       : angle       4.20482 (  981)
  covalent geometry    : bond        0.00262 ( 9108)
  covalent geometry    : angle       0.66504 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 94
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6426 (t80)
REVERT: A   87 LEU cc_start: 0.3675 (OUTLIER) cc_final: 0.3359 (tt)
REVERT: A  171 PHE cc_start: 0.6998 (p90) cc_final: 0.6601 (p90)
REVERT: A  225 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5699 (mt-10)
REVERT: A  303 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7229 (ptm160)
REVERT: A  420 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7099 (mt)
REVERT: A  736 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6180 (ttm-80)
REVERT: A  744 GLU cc_start: 0.4772 (OUTLIER) cc_final: 0.3916 (mp0)
REVERT: B  377 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7579 (mp)
REVERT: B  479 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6466 (mt)
REVERT: B  672 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.3982 (mm)
  outliers start: 51
  outliers final: 35
  residues processed: 139
  average time/residue: 0.2257
  time to fit residues: 42.8045
Evaluate side-chains
  137 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 92
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  672 LEU
Chi-restraints excluded: chain B residue  690 CYS
Chi-restraints excluded: chain B residue  723 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0870
   chunk 32 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 48 optimal weight:   30.0000
   chunk 106 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0970
   overall best weight:    1.1960

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

Flipped N/Q/H residues before XYZ refinement:
A 723 HIS
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 371 GLN
B 723 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.248788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.213160 restraints weight = 9830.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4512 rms_B_bonded: 2.86
r_work: 0.4328 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4356 r_free = 0.4356    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4356 r_free = 0.4356    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.4356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9108  Z= 0.154
  Angle     :  0.713  14.588  12384  Z= 0.337
  Chirality :  0.044   0.180   1412
  Planarity :  0.005   0.048   1604
  Dihedral  :  4.295  18.055   1262
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 30.50 %
    Favored  : 64.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.71 (0.26), residues: 1136
  helix:  0.58 (0.24), residues: 486
  sheet: -0.94 (0.51), residues: 110
  loop : -1.34 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 403 
 HIS   0.004   0.001   HIS B 160 
 PHE   0.009   0.001   PHE A  37 
 TYR   0.019   0.002   TYR B 156 
 ARG   0.006   0.000   ARG B 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 (  330)
  hydrogen bonds       : angle       4.39868 (  981)
  covalent geometry    : bond        0.00368 ( 9108)
  covalent geometry    : angle       0.71275 (12384)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 96
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6689 (t80)
REVERT: A   87 LEU cc_start: 0.3625 (OUTLIER) cc_final: 0.3319 (tt)
REVERT: A  171 PHE cc_start: 0.6999 (p90) cc_final: 0.6569 (p90)
REVERT: A  182 GLN cc_start: 0.7114 (mp10) cc_final: 0.6744 (mp10)
REVERT: A  225 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5731 (mt-10)
REVERT: A  303 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7412 (ptm160)
REVERT: A  341 ARG cc_start: 0.5058 (tpm170) cc_final: 0.4806 (tpt170)
REVERT: A  420 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7337 (mt)
REVERT: A  736 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6090 (ttm-80)
REVERT: A  744 GLU cc_start: 0.4927 (OUTLIER) cc_final: 0.4067 (mp0)
REVERT: B  303 ARG cc_start: 0.7605 (ptm-80) cc_final: 0.7274 (ptm160)
REVERT: B  341 ARG cc_start: 0.5185 (tpm170) cc_final: 0.4983 (mmp-170)
REVERT: B  377 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: B  479 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6694 (mt)
REVERT: B  672 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4185 (mm)
  outliers start: 52
  outliers final: 37
  residues processed: 140
  average time/residue: 0.2393
  time to fit residues: 45.5621
Evaluate side-chains
  140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 93
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  693 ASP
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  164 PHE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  397 CYS
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  482 CYS
Chi-restraints excluded: chain B residue  672 LEU
Chi-restraints excluded: chain B residue  688 VAL
Chi-restraints excluded: chain B residue  690 CYS
Chi-restraints excluded: chain B residue  723 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 723 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.249512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.213729 restraints weight = 9849.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.4527 rms_B_bonded: 2.87
r_work: 0.4357 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4364 r_free = 0.4364    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4364 r_free = 0.4364    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.4364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5903
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9108  Z= 0.144
  Angle     :  0.705  14.381  12384  Z= 0.333
  Chirality :  0.044   0.183   1412
  Planarity :  0.005   0.048   1604
  Dihedral  :  4.268  17.565   1262
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 30.82 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.70 (0.26), residues: 1136
  helix:  0.60 (0.24), residues: 486
  sheet: -0.89 (0.52), residues: 110
  loop : -1.35 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 403 
 HIS   0.005   0.001   HIS B 723 
 PHE   0.007   0.001   PHE B 354 
 TYR   0.018   0.002   TYR B 156 
 ARG   0.004   0.000   ARG B 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04286 (  330)
  hydrogen bonds       : angle       4.37722 (  981)
  covalent geometry    : bond        0.00343 ( 9108)
  covalent geometry    : angle       0.70452 (12384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4481.32 seconds
wall clock time: 77 minutes 52.32 seconds (4672.32 seconds total)