Starting phenix.real_space_refine
on Sat Aug 23 01:15:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hbf_34627/08_2025/8hbf_34627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hbf_34627/08_2025/8hbf_34627.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hbf_34627/08_2025/8hbf_34627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hbf_34627/08_2025/8hbf_34627.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hbf_34627/08_2025/8hbf_34627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hbf_34627/08_2025/8hbf_34627.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.002 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: 8
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P       3      5.49       5
     Mg      2      5.21       5
     S      58      5.16       5
     C    5438      2.51       5
     N    1434      2.21       5
     O    1511      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8448
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 522, 3894
          Classifications: {'peptide': 522}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 23, 'TRANS': 498}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 238
          Unresolved non-hydrogen angles: 286
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 15, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 158
    Chain: "B"
      Number of atoms: 4444
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 573, 4442
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 106
          Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 101
      Conformer: "B"
        Number of residues, atoms: 573, 4442
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 106
          Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 101
          bond proxies already assigned to first conformer: 4530
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {' MG': 2, 'G2P': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {' NO': 1, 'GZO': 1, 'HEM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.44, per 1000 atoms: 0.29
  Number of scatterers: 8448
  At special positions: 0
  Unit cell: (65.835, 107.635, 150.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Fe      1     26.01
     S      58     16.00
     P       3     15.00
     Mg      2     11.99
     F       1      9.00
     O    1511      8.00
     N    1434      7.00
     C    5438      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 474.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2060

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      50.1% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
      removed outlier: 3.674A  pdb=" N   LEU A  74 " --> pdb=" O   TYR A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 98
      removed outlier: 3.628A  pdb=" N   GLN A  94 " --> pdb=" O   ASN A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 128 through 149
      removed outlier: 3.787A  pdb=" N   ILE A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
      removed outlier: 3.665A  pdb=" N   VAL A 154 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.716A  pdb=" N   PHE A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 302 through 309
      removed outlier: 3.763A  pdb=" N   LEU A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 323
      removed outlier: 3.778A  pdb=" N   TYR A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 319 through 323'
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 404 through 407
    Processing helix  chain 'A' and resid 408 through 458
      removed outlier: 3.719A  pdb=" N   VAL A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR A 450 " --> pdb=" O   GLU A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 468
    Processing helix  chain 'A' and resid 489 through 497
    Processing helix  chain 'A' and resid 498 through 521
      removed outlier: 3.783A  pdb=" N   ARG A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 561
      removed outlier: 4.122A  pdb=" N   ASP A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 610
      removed outlier: 3.728A  pdb=" N   THR A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 627
    Processing helix  chain 'A' and resid 638 through 642
      removed outlier: 3.839A  pdb=" N   LEU A 642 " --> pdb=" O   ARG A 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 4.167A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 29
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.861A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 81
      removed outlier: 3.944A  pdb=" N   LYS B  72 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET B  73 " --> pdb=" O   MET B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 90
      removed outlier: 3.752A  pdb=" N   LEU B  90 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 100
    Processing helix  chain 'B' and resid 100 through 112
    Processing helix  chain 'B' and resid 144 through 159
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 233 through 240
      removed outlier: 3.545A  pdb=" N   ARG B 238 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 244
    Processing helix  chain 'B' and resid 249 through 253
      removed outlier: 3.661A  pdb=" N   VAL B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 253'
    Processing helix  chain 'B' and resid 264 through 271
      removed outlier: 3.856A  pdb=" N   HIS B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 336
      removed outlier: 3.535A  pdb=" N   ARG B 336 " --> pdb=" O   ASP B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 398
      removed outlier: 3.566A  pdb=" N   GLU B 370 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 408
      removed outlier: 4.004A  pdb=" N   GLU B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
    Processing helix  chain 'B' and resid 441 through 461
      removed outlier: 3.756A  pdb=" N   THR B 455 " --> pdb=" O   ASN B 451 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG B 456 " --> pdb=" O   ASP B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 507
      removed outlier: 3.530A  pdb=" N   SER B 495 " --> pdb=" O   HIS B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.777A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 573
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193
      removed outlier: 3.841A  pdb=" N   HIS A 201 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300
      removed outlier: 6.775A  pdb=" N   MET A 291 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 526
      removed outlier: 7.155A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 523 through 526
      removed outlier: 7.155A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ILE A 616 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL A 633 " --> pdb=" O   ASP A 658 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124
      removed outlier: 3.677A  pdb=" N   GLU B 182 " --> pdb=" O   ASP B 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.615A  pdb=" N   ARG B 279 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   LEU B 256 " --> pdb=" O   ARG B 279 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 470 through 473
      removed outlier: 7.025A  pdb=" N   MET B 480 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR B 421 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG B 416 " --> pdb=" O   THR B 530 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   THR B 530 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   ASP B 418 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   VAL B 528 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 473
      removed outlier: 7.025A  pdb=" N   MET B 480 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR B 421 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ARG B 416 " --> pdb=" O   THR B 530 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   THR B 530 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   ASP B 418 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   VAL B 528 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE B 562 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   MET B 599 " --> pdb=" O   PRO B 589 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL B 601 " --> pdb=" O   ARG B 587 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 511 through 512

    510 hydrogen bonds defined for protein.
    1458 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: 1.20

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.18 -     1.36: 2763
        1.36 -     1.55: 5755
        1.55 -     1.73: 8
        1.73 -     1.91: 91
        1.91 -     2.09: 3
  Bond restraints: 8620
  Sorted by residual:
  bond pdb=" C13 GZO B 702 "
       pdb=" N06 GZO B 702 "
    ideal  model  delta    sigma   weight residual
    1.327  1.535 -0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C17 GZO B 702 "
       pdb=" N07 GZO B 702 "
    ideal  model  delta    sigma   weight residual
    1.322  1.476 -0.154 2.00e-02 2.50e+03 5.96e+01
  bond pdb=" C17 GZO B 702 "
       pdb=" N08 GZO B 702 "
    ideal  model  delta    sigma   weight residual
    1.321  1.473 -0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" C12 GZO B 702 "
       pdb=" C18 GZO B 702 "
    ideal  model  delta    sigma   weight residual
    1.397  1.536 -0.139 2.00e-02 2.50e+03 4.85e+01
  bond pdb=" C25 GZO B 702 "
       pdb=" N06 GZO B 702 "
    ideal  model  delta    sigma   weight residual
    1.319  1.456 -0.137 2.00e-02 2.50e+03 4.66e+01
  ... (remaining 8615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 11462
        2.47 -     4.93: 205
        4.93 -     7.40: 32
        7.40 -     9.87: 12
        9.87 -    12.33: 4
  Bond angle restraints: 11715
  Sorted by residual:
  angle pdb=" N   ALA A 659 "
        pdb=" CA  ALA A 659 "
        pdb=" C   ALA A 659 "
      ideal   model   delta    sigma   weight residual
     109.07  119.88  -10.81 1.52e+00 4.33e-01 5.06e+01
  angle pdb=" N   TRP A 467 "
        pdb=" CA  TRP A 467 "
        pdb=" C   TRP A 467 "
      ideal   model   delta    sigma   weight residual
     111.07  103.85    7.22 1.07e+00 8.73e-01 4.56e+01
  angle pdb=" C   TRP A 467 "
        pdb=" CA  TRP A 467 "
        pdb=" CB  TRP A 467 "
      ideal   model   delta    sigma   weight residual
     110.88  102.33    8.55 1.57e+00 4.06e-01 2.97e+01
  angle pdb=" CA  TRP A 467 "
        pdb=" CB  TRP A 467 "
        pdb=" CG  TRP A 467 "
      ideal   model   delta    sigma   weight residual
     113.60  122.81   -9.21 1.90e+00 2.77e-01 2.35e+01
  angle pdb=" N   ASP A 658 "
        pdb=" CA  ASP A 658 "
        pdb=" C   ASP A 658 "
      ideal   model   delta    sigma   weight residual
     111.36  116.26   -4.90 1.09e+00 8.42e-01 2.02e+01
  ... (remaining 11710 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 4494
       17.19 -    34.38: 458
       34.38 -    51.57: 154
       51.57 -    68.75: 15
       68.75 -    85.94: 13
  Dihedral angle restraints: 5134
    sinusoidal: 1956
      harmonic: 3178
  Sorted by residual:
  dihedral pdb=" CA  ALA A 659 "
           pdb=" C   ALA A 659 "
           pdb=" N   TYR A 660 "
           pdb=" CA  TYR A 660 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" C   TRP A 467 "
           pdb=" N   TRP A 467 "
           pdb=" CA  TRP A 467 "
           pdb=" CB  TRP A 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.96  -11.64     0      2.50e+00 1.60e-01 2.17e+01
  dihedral pdb=" CA  HIS A 406 "
           pdb=" C   HIS A 406 "
           pdb=" N   ASN A 407 "
           pdb=" CA  ASN A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.00  -23.00     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 5131 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1122
       0.061 -    0.121: 219
       0.121 -    0.182: 20
       0.182 -    0.242: 6
       0.242 -    0.303: 2
  Chirality restraints: 1369
  Sorted by residual:
  chirality pdb=" CA  LYS B 409 "
            pdb=" N   LYS B 409 "
            pdb=" C   LYS B 409 "
            pdb=" CB  LYS B 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  ASN B 404 "
            pdb=" N   ASN B 404 "
            pdb=" C   ASN B 404 "
            pdb=" CB  ASN B 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  GLU B 405 "
            pdb=" N   GLU B 405 "
            pdb=" C   GLU B 405 "
            pdb=" CB  GLU B 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1366 not shown)

  Planarity restraints: 1471
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 657 "   -0.017 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   LEU A 657 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LEU A 657 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 658 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 410 "   -0.039 5.00e-02 4.00e+02   5.89e-02 5.56e+00
        pdb=" N   PRO B 411 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B 411 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 411 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 574 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO B 575 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 575 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 575 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1468 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 46
        2.54 -     3.13: 6458
        3.13 -     3.72: 12923
        3.72 -     4.31: 18271
        4.31 -     4.90: 31659
  Nonbonded interactions: 69357
  Sorted by model distance:
  nonbonded pdb=" O5' G2P A1001 "
            pdb="MG    MG A1002 "
     model   vdw
     1.951 2.170
  nonbonded pdb=" O3B G2P A1001 "
            pdb="MG    MG A1003 "
     model   vdw
     2.050 2.170
  nonbonded pdb=" O   SER B 249 "
            pdb=" OG  SER B 252 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   GLY A 337 "
            pdb=" OG1 THR A 340 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ILE B 111 "
            pdb=" NH2 ARG B 360 "
     model   vdw
     2.214 3.120
  ... (remaining 69352 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.820
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
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      :  0.011   0.368   8621  Z= 0.467
  Angle     :  0.845  12.335  11715  Z= 0.431
  Chirality :  0.049   0.303   1369
  Planarity :  0.005   0.059   1471
  Dihedral  : 15.942  85.944   3074
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.18 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 20.82 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.25), residues: 1069
  helix:  0.46 (0.23), residues: 512
  sheet: -0.11 (0.35), residues: 222
  loop : -0.94 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 570 
 TYR   0.018   0.002   TYR B 112 
 PHE   0.018   0.002   PHE B  75 
 TRP   0.021   0.004   TRP A 467 
 HIS   0.008   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00976 ( 8620)
  covalent geometry    : angle       0.84478 (11715)
  hydrogen bonds       : bond        0.14907 (  477)
  hydrogen bonds       : angle       7.02237 ( 1458)
  Misc. bond           : bond        0.36751 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  253 LEU cc_start: 0.8330 (mt) cc_final: 0.8077 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 100
  average time/residue: 0.0657
  time to fit residues: 10.0251
Evaluate side-chains
  97 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain B residue   56 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.0020
   chunk 49 optimal weight:    0.0970
   chunk 97 optimal weight:    0.0170
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.2624

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
A 470 GLN
A 600 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.164021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133939 restraints weight = 11910.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.90
r_work: 0.3408 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.241   8621  Z= 0.122
  Angle     :  0.560   8.187  11715  Z= 0.293
  Chirality :  0.042   0.143   1369
  Planarity :  0.004   0.053   1471
  Dihedral  :  6.650  79.872   1207
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.34 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1069
  helix:  1.49 (0.23), residues: 505
  sheet: -0.24 (0.34), residues: 229
  loop : -0.92 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 570 
 TYR   0.017   0.001   TYR B 479 
 PHE   0.017   0.001   PHE B  75 
 TRP   0.009   0.002   TRP B  22 
 HIS   0.003   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8620)
  covalent geometry    : angle       0.56014 (11715)
  hydrogen bonds       : bond        0.04751 (  477)
  hydrogen bonds       : angle       4.78963 ( 1458)
  Misc. bond           : bond        0.24087 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.7826 (m-80) cc_final: 0.7617 (m-80)
REVERT: A  335 PHE cc_start: 0.7735 (t80) cc_final: 0.7345 (t80)
REVERT: A  370 MET cc_start: 0.8194 (mtt) cc_final: 0.7975 (mtt)
REVERT: A  458 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6260 (p90)
REVERT: B   93 ASN cc_start: 0.7941 (t0) cc_final: 0.7681 (t0)
REVERT: B  360 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7768 (tpp-160)
REVERT: B  570 ARG cc_start: 0.7584 (mtt90) cc_final: 0.6885 (mtt90)
  outliers start: 17
  outliers final: 8
  residues processed: 117
  average time/residue: 0.0645
  time to fit residues: 11.4283
Evaluate side-chains
  107 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  467 TRP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 102 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 17 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
B 466 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.165310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.136445 restraints weight = 12317.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.11
r_work: 0.3368 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.273   8621  Z= 0.126
  Angle     :  0.543   8.549  11715  Z= 0.280
  Chirality :  0.042   0.150   1369
  Planarity :  0.004   0.052   1471
  Dihedral  :  6.515  76.154   1206
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.02 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.26), residues: 1069
  helix:  1.80 (0.23), residues: 505
  sheet: -0.20 (0.33), residues: 229
  loop : -0.85 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.015   0.001   TYR B 112 
 PHE   0.016   0.001   PHE B  75 
 TRP   0.012   0.002   TRP A 467 
 HIS   0.004   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8620)
  covalent geometry    : angle       0.54272 (11715)
  hydrogen bonds       : bond        0.04423 (  477)
  hydrogen bonds       : angle       4.45603 ( 1458)
  Misc. bond           : bond        0.27345 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7371 (m-70)
REVERT: A  335 PHE cc_start: 0.7754 (t80) cc_final: 0.7425 (t80)
REVERT: A  443 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7849 (tt)
REVERT: B   93 ASN cc_start: 0.7956 (t0) cc_final: 0.7710 (t0)
REVERT: B  279 ARG cc_start: 0.8587 (ttt-90) cc_final: 0.8305 (ttp80)
REVERT: B  360 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7917 (tpp-160)
REVERT: B  570 ARG cc_start: 0.7619 (mtt90) cc_final: 0.6962 (mtt90)
  outliers start: 19
  outliers final: 10
  residues processed: 118
  average time/residue: 0.0684
  time to fit residues: 12.0105
Evaluate side-chains
  109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
A 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.163669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.133372 restraints weight = 12392.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.93
r_work: 0.3401 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.324   8621  Z= 0.131
  Angle     :  0.540   8.708  11715  Z= 0.276
  Chirality :  0.042   0.150   1369
  Planarity :  0.004   0.051   1471
  Dihedral  :  6.441  72.103   1206
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.71 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1069
  helix:  1.87 (0.23), residues: 505
  sheet: -0.08 (0.34), residues: 224
  loop : -0.93 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 570 
 TYR   0.014   0.001   TYR B 479 
 PHE   0.015   0.001   PHE B  75 
 TRP   0.012   0.002   TRP A 467 
 HIS   0.004   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8620)
  covalent geometry    : angle       0.53990 (11715)
  hydrogen bonds       : bond        0.04305 (  477)
  hydrogen bonds       : angle       4.37256 ( 1458)
  Misc. bond           : bond        0.32375 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  150 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6877 (m-40)
REVERT: A  258 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7435 (m-70)
REVERT: A  335 PHE cc_start: 0.7628 (t80) cc_final: 0.7150 (t80)
REVERT: A  473 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7623 (mp-120)
REVERT: B   93 ASN cc_start: 0.7902 (t0) cc_final: 0.7662 (t0)
REVERT: B  279 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8261 (ttp80)
REVERT: B  360 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7864 (tpp-160)
REVERT: B  570 ARG cc_start: 0.7579 (mtt90) cc_final: 0.6895 (mtt90)
REVERT: B  600 GLN cc_start: 0.7930 (mt0) cc_final: 0.7451 (mm-40)
  outliers start: 21
  outliers final: 13
  residues processed: 124
  average time/residue: 0.0718
  time to fit residues: 12.7037
Evaluate side-chains
  115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  473 GLN
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:    0.2980
   chunk 93 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.164507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.136138 restraints weight = 12445.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.98
r_work: 0.3398 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.361   8621  Z= 0.139
  Angle     :  0.543   8.738  11715  Z= 0.277
  Chirality :  0.042   0.161   1369
  Planarity :  0.004   0.050   1471
  Dihedral  :  6.446  70.061   1206
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.05 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.26), residues: 1069
  helix:  1.88 (0.23), residues: 505
  sheet: -0.05 (0.34), residues: 224
  loop : -0.93 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 570 
 TYR   0.013   0.001   TYR B 479 
 PHE   0.014   0.001   PHE B  75 
 TRP   0.013   0.002   TRP A 467 
 HIS   0.004   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8620)
  covalent geometry    : angle       0.54275 (11715)
  hydrogen bonds       : bond        0.04303 (  477)
  hydrogen bonds       : angle       4.36409 ( 1458)
  Misc. bond           : bond        0.36061 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7447 (m-70)
REVERT: A  335 PHE cc_start: 0.7641 (t80) cc_final: 0.7141 (t80)
REVERT: A  473 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7662 (mp-120)
REVERT: B   93 ASN cc_start: 0.7931 (t0) cc_final: 0.7698 (t0)
REVERT: B  279 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.8264 (ttp80)
REVERT: B  360 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7877 (tpp-160)
REVERT: B  600 GLN cc_start: 0.7918 (mt0) cc_final: 0.7672 (mp10)
  outliers start: 24
  outliers final: 16
  residues processed: 123
  average time/residue: 0.0691
  time to fit residues: 12.4112
Evaluate side-chains
  116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  473 GLN
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0070
   chunk 21 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0770
   chunk 77 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
B 563 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.163534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132969 restraints weight = 12360.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.95
r_work: 0.3404 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.288   8621  Z= 0.116
  Angle     :  0.522   8.614  11715  Z= 0.265
  Chirality :  0.041   0.160   1369
  Planarity :  0.004   0.050   1471
  Dihedral  :  6.118  68.430   1204
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.96 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1069
  helix:  1.97 (0.23), residues: 507
  sheet: -0.03 (0.34), residues: 222
  loop : -0.91 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.014   0.001   TYR B 479 
 PHE   0.014   0.001   PHE B  75 
 TRP   0.012   0.002   TRP A 467 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8620)
  covalent geometry    : angle       0.52246 (11715)
  hydrogen bonds       : bond        0.04091 (  477)
  hydrogen bonds       : angle       4.27080 ( 1458)
  Misc. bond           : bond        0.28789 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7471 (m-70)
REVERT: A  335 PHE cc_start: 0.7632 (t80) cc_final: 0.7040 (t80)
REVERT: B  279 ARG cc_start: 0.8501 (ttt-90) cc_final: 0.8243 (ttp80)
REVERT: B  360 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7888 (tpp-160)
REVERT: B  600 GLN cc_start: 0.7865 (mt0) cc_final: 0.7494 (mm-40)
  outliers start: 21
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0713
  time to fit residues: 11.9684
Evaluate side-chains
  110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
B 563 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.160850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131291 restraints weight = 17042.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.22
r_work: 0.3349 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.389   8621  Z= 0.163
  Angle     :  0.567   8.808  11715  Z= 0.289
  Chirality :  0.042   0.159   1369
  Planarity :  0.004   0.049   1471
  Dihedral  :  6.179  65.414   1204
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.07 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1069
  helix:  1.94 (0.23), residues: 505
  sheet: -0.07 (0.33), residues: 224
  loop : -0.85 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 570 
 TYR   0.014   0.001   TYR B 479 
 PHE   0.014   0.002   PHE B  75 
 TRP   0.014   0.002   TRP A 467 
 HIS   0.005   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8620)
  covalent geometry    : angle       0.56685 (11715)
  hydrogen bonds       : bond        0.04355 (  477)
  hydrogen bonds       : angle       4.32311 ( 1458)
  Misc. bond           : bond        0.38868 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7491 (m-70)
REVERT: A  335 PHE cc_start: 0.7712 (t80) cc_final: 0.7110 (t80)
REVERT: A  502 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8267 (p)
REVERT: A  590 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7631 (ttmm)
REVERT: B   93 ASN cc_start: 0.7944 (t0) cc_final: 0.7731 (t0)
REVERT: B  360 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7978 (tpp-160)
REVERT: B  600 GLN cc_start: 0.8007 (mt0) cc_final: 0.7599 (mm-40)
  outliers start: 25
  outliers final: 17
  residues processed: 120
  average time/residue: 0.0944
  time to fit residues: 15.9872
Evaluate side-chains
  114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.160953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.131463 restraints weight = 10008.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.69
r_work: 0.3408 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.344   8621  Z= 0.137
  Angle     :  0.545   8.721  11715  Z= 0.278
  Chirality :  0.042   0.159   1369
  Planarity :  0.004   0.049   1471
  Dihedral  :  6.150  64.731   1204
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.18 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1069
  helix:  1.98 (0.23), residues: 505
  sheet: -0.08 (0.34), residues: 224
  loop : -0.87 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 570 
 TYR   0.015   0.001   TYR B 211 
 PHE   0.014   0.001   PHE B  75 
 TRP   0.012   0.002   TRP A 467 
 HIS   0.004   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8620)
  covalent geometry    : angle       0.54505 (11715)
  hydrogen bonds       : bond        0.04230 (  477)
  hydrogen bonds       : angle       4.29837 ( 1458)
  Misc. bond           : bond        0.34392 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7472 (m-70)
REVERT: A  335 PHE cc_start: 0.7658 (t80) cc_final: 0.7044 (t80)
REVERT: A  502 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8169 (p)
REVERT: A  590 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7562 (ttmm)
REVERT: B   93 ASN cc_start: 0.7815 (t0) cc_final: 0.7600 (t0)
REVERT: B  360 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7834 (tpp-160)
REVERT: B  600 GLN cc_start: 0.7940 (mt0) cc_final: 0.7570 (mm-40)
  outliers start: 23
  outliers final: 17
  residues processed: 117
  average time/residue: 0.0891
  time to fit residues: 15.0126
Evaluate side-chains
  113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0770
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0370
   chunk 50 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0470
   chunk 94 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.3114

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
B 266 HIS
B 563 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.164286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.135203 restraints weight = 11910.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.13
r_work: 0.3434 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3307
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.205   8621  Z= 0.102
  Angle     :  0.513   8.519  11715  Z= 0.261
  Chirality :  0.041   0.157   1369
  Planarity :  0.004   0.049   1471
  Dihedral  :  5.987  65.173   1204
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.30 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.26), residues: 1069
  helix:  2.12 (0.24), residues: 508
  sheet:  0.05 (0.34), residues: 229
  loop : -0.94 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 570 
 TYR   0.015   0.001   TYR B 211 
 PHE   0.015   0.001   PHE B 223 
 TRP   0.008   0.002   TRP A 467 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8620)
  covalent geometry    : angle       0.51277 (11715)
  hydrogen bonds       : bond        0.03852 (  477)
  hydrogen bonds       : angle       4.15540 ( 1458)
  Misc. bond           : bond        0.20547 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.7547 (m-70)
REVERT: A  335 PHE cc_start: 0.7689 (t80) cc_final: 0.7114 (t80)
REVERT: A  458 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7439 (p90)
REVERT: A  590 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7544 (ttmm)
  outliers start: 20
  outliers final: 12
  residues processed: 119
  average time/residue: 0.0840
  time to fit residues: 14.6145
Evaluate side-chains
  111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0050
   chunk 61 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 600 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.163353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133341 restraints weight = 10082.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.80
r_work: 0.3409 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.249   8621  Z= 0.119
  Angle     :  0.539   8.909  11715  Z= 0.271
  Chirality :  0.041   0.158   1369
  Planarity :  0.004   0.049   1471
  Dihedral  :  5.978  62.808   1204
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 23.09 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.26), residues: 1069
  helix:  2.13 (0.23), residues: 509
  sheet:  0.07 (0.34), residues: 229
  loop : -0.87 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 570 
 TYR   0.014   0.001   TYR B 479 
 PHE   0.014   0.001   PHE B  75 
 TRP   0.010   0.002   TRP A 467 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8620)
  covalent geometry    : angle       0.53949 (11715)
  hydrogen bonds       : bond        0.03968 (  477)
  hydrogen bonds       : angle       4.14447 ( 1458)
  Misc. bond           : bond        0.24929 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  258 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7667 (m-70)
REVERT: A  335 PHE cc_start: 0.7709 (t80) cc_final: 0.7125 (t80)
REVERT: A  364 MET cc_start: 0.7757 (ptm) cc_final: 0.7401 (ttp)
REVERT: A  590 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7568 (ttmm)
REVERT: B   73 MET cc_start: 0.8274 (tpp) cc_final: 0.7989 (tpp)
  outliers start: 16
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0821
  time to fit residues: 13.1843
Evaluate side-chains
  109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  547 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  541 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.162439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.132611 restraints weight = 16860.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.73
r_work: 0.3342 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.277   8621  Z= 0.129
  Angle     :  0.545   8.824  11715  Z= 0.274
  Chirality :  0.041   0.148   1369
  Planarity :  0.004   0.049   1471
  Dihedral  :  5.998  61.967   1204
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.53 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1069
  helix:  2.10 (0.23), residues: 508
  sheet:  0.06 (0.33), residues: 229
  loop : -0.82 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 570 
 TYR   0.016   0.001   TYR A 145 
 PHE   0.014   0.001   PHE B 223 
 TRP   0.011   0.002   TRP A 467 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8620)
  covalent geometry    : angle       0.54540 (11715)
  hydrogen bonds       : bond        0.04055 (  477)
  hydrogen bonds       : angle       4.16732 ( 1458)
  Misc. bond           : bond        0.27734 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2486.61 seconds
wall clock time: 43 minutes 13.49 seconds (2593.49 seconds total)