Starting phenix.real_space_refine
on Mon Jul 28 20:02:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m5v_30094/07_2025/6m5v_30094.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m5v_30094/07_2025/6m5v_30094.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m5v_30094/07_2025/6m5v_30094.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m5v_30094/07_2025/6m5v_30094.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m5v_30094/07_2025/6m5v_30094.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m5v_30094/07_2025/6m5v_30094.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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: 9
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      47      5.16       5
     Be      1      3.05       5
     C    6703      2.51       5
     N    1893      2.21       5
     O    1897      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10549
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4482
          Classifications: {'peptide': 585}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 29, 'TRANS': 555}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 5208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 670, 5208
          Classifications: {'peptide': 670}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 33, 'TRANS': 636}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 825
          Classifications: {'peptide': 104}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 99}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5415  SG  CYS B 121      31.477  46.241  53.912  1.00 47.42           S
  ATOM  10277  SG  CYS C 101      30.191  46.342  57.304  1.00 59.52           S
  ATOM   6010  SG  CYS B 197      52.449  54.153  49.925  1.00 43.06           S
  ATOM   6028  SG  CYS B 200      54.145  55.532  52.620  1.00 41.30           S

  Time building chain proxies: 6.28, per 1000 atoms: 0.60
  Number of scatterers: 10549
  At special positions: 0
  Unit cell: (108.16, 101.92, 120.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Zn      2     29.99
     S      47     16.00
     P       2     15.00
     Mg      1     11.99
     F       3      9.00
     O    1897      8.00
     N    1893      7.00
     C    6703      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 801 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS B 121 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS C 101 "
      pdb="  ZN B 802 "
        pdb="ZN    ZN B 802 " - pdb=" SG  CYS B 200 "
        pdb="ZN    ZN B 802 " - pdb=" SG  CYS B 197 "


  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2566

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      53.3% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 73 through 81
      removed outlier: 4.300A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 3.539A  pdb=" N   PHE A  85 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   SER A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A  89 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 118
    Processing helix  chain 'A' and resid 129 through 149
      removed outlier: 3.731A  pdb=" N   GLN A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 167
      removed outlier: 3.741A  pdb=" N   ASP A 162 " --> pdb=" O   HIS A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 203 through 221
      removed outlier: 4.173A  pdb=" N   LEU A 209 " --> pdb=" O   GLN A 205 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 215 " --> pdb=" O   HIS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 236
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 3.673A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.710A  pdb=" N   VAL A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 365 through 373
      removed outlier: 4.180A  pdb=" N   ILE A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 489
    Processing helix  chain 'A' and resid 496 through 500
    Processing helix  chain 'A' and resid 549 through 569
    Processing helix  chain 'A' and resid 585 through 601
    Processing helix  chain 'A' and resid 639 through 653
    Processing helix  chain 'A' and resid 672 through 682
    Processing helix  chain 'A' and resid 706 through 719
    Processing helix  chain 'B' and resid 6 through 33
      removed outlier: 3.613A  pdb=" N   VAL B  10 " --> pdb=" O   SER B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'B' and resid 61 through 70
    Processing helix  chain 'B' and resid 74 through 101
    Processing helix  chain 'B' and resid 106 through 115
      removed outlier: 3.598A  pdb=" N   PHE B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 156
      removed outlier: 3.633A  pdb=" N   VAL B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 180
      removed outlier: 3.818A  pdb=" N   PHE B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY B 178 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 191
      removed outlier: 3.788A  pdb=" N   SER B 191 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 205
      removed outlier: 3.786A  pdb=" N   PHE B 201 " --> pdb=" O   CYS B 197 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 237 through 243
      removed outlier: 3.525A  pdb=" N   TYR B 242 " --> pdb=" O   GLU B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 265
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.104A  pdb=" N   GLN B 312 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 355
    Processing helix  chain 'B' and resid 374 through 381
      removed outlier: 3.764A  pdb=" N   ILE B 381 " --> pdb=" O   ASP B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 400
      removed outlier: 3.867A  pdb=" N   ALA B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 414
    Processing helix  chain 'B' and resid 414 through 429
      removed outlier: 3.554A  pdb=" N   CYS B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 510
      removed outlier: 3.557A  pdb=" N   LEU B 502 " --> pdb=" O   GLU B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 531
      removed outlier: 3.542A  pdb=" N   MET B 529 " --> pdb=" O   GLU B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 560
      removed outlier: 3.741A  pdb=" N   GLY B 549 " --> pdb=" O   ALA B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 587
      removed outlier: 3.936A  pdb=" N   ALA B 578 " --> pdb=" O   GLY B 574 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE B 581 " --> pdb=" O   ASP B 577 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   MET B 582 " --> pdb=" O   ALA B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 594
      No H-bonds generated for 'chain 'B' and resid 592 through 594'
    Processing helix  chain 'B' and resid 595 through 608
      removed outlier: 4.314A  pdb=" N   HIS B 601 " --> pdb=" O   PRO B 597 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE B 604 " --> pdb=" O   THR B 600 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU B 606 " --> pdb=" O   ARG B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 633
      removed outlier: 3.912A  pdb=" N   SER B 630 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 646
      removed outlier: 3.643A  pdb=" N   GLU B 642 " --> pdb=" O   PRO B 638 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLU B 643 " --> pdb=" O   HIS B 639 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 644 " --> pdb=" O   LEU B 640 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA B 645 " --> pdb=" O   LYS B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 675 through 700
      removed outlier: 3.534A  pdb=" N   GLN B 679 " --> pdb=" O   ILE B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 760 through 772
      removed outlier: 3.700A  pdb=" N   LEU B 769 " --> pdb=" O   LEU B 765 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 35
      removed outlier: 3.632A  pdb=" N   LEU C  30 " --> pdb=" O   THR C  26 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 80
      removed outlier: 3.627A  pdb=" N   LEU C  78 " --> pdb=" O   ARG C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 128
      removed outlier: 3.676A  pdb=" N   GLU C 105 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA C 116 " --> pdb=" O   GLU C 112 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   HIS C 125 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 386
      removed outlier: 7.623A  pdb=" N   THR A 254 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   SER A 384 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   PHE A 256 " --> pdb=" O   SER A 384 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   THR A 386 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A 258 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 255 " --> pdb=" O   ASN A 408 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316
      removed outlier: 3.656A  pdb=" N   SER A 332 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 619
      removed outlier: 6.119A  pdb=" N   VAL A 576 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU A 504 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   ALA A 579 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A 506 " --> pdb=" O   ALA A 579 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASP A 503 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   ARG A 528 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   THR A 521 " --> pdb=" O   HIS A 540 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   HIS A 540 " --> pdb=" O   THR A 521 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL A 523 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU A 538 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   TYR A 533 " --> pdb=" O   MET A 657 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   SER A 659 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ILE A 535 " --> pdb=" O   SER A 659 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLU A 661 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA A 537 " --> pdb=" O   GLU A 661 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL A 663 " --> pdb=" O   ALA A 537 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   GLU A 539 " --> pdb=" O   VAL A 663 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126
    Processing sheet with id=AA7, first strand: chain 'B' and resid 566 through 568
      removed outlier: 6.363A  pdb=" N   ILE B 567 " --> pdb=" O   TYR B 757 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL B 738 " --> pdb=" O   TYR B 728 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1452 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.07

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1691
        1.30 -     1.43: 2872
        1.43 -     1.56: 6132
        1.56 -     1.68: 13
        1.68 -     1.81: 68
  Bond restraints: 10776
  Sorted by residual:
  bond pdb=" F3  BEF A 802 "
       pdb="BE   BEF A 802 "
    ideal  model  delta    sigma   weight residual
    1.476  1.765 -0.289 2.00e-02 2.50e+03 2.09e+02
  bond pdb=" F1  BEF A 802 "
       pdb="BE   BEF A 802 "
    ideal  model  delta    sigma   weight residual
    1.476  1.765 -0.289 2.00e-02 2.50e+03 2.08e+02
  bond pdb=" F2  BEF A 802 "
       pdb="BE   BEF A 802 "
    ideal  model  delta    sigma   weight residual
    1.476  1.764 -0.288 2.00e-02 2.50e+03 2.08e+02
  bond pdb=" C   ALA A 482 "
       pdb=" O   ALA A 482 "
    ideal  model  delta    sigma   weight residual
    1.237  1.172  0.064 1.17e-02 7.31e+03 3.02e+01
  bond pdb=" C4  ADP A 801 "
       pdb=" C5  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.01e+01
  ... (remaining 10771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 14168
        2.17 -     4.34: 411
        4.34 -     6.50: 48
        6.50 -     8.67: 12
        8.67 -    10.84: 4
  Bond angle restraints: 14643
  Sorted by residual:
  angle pdb=" C   CYS A 125 "
        pdb=" N   ALA A 126 "
        pdb=" CA  ALA A 126 "
      ideal   model   delta    sigma   weight residual
     122.52  130.37   -7.85 1.16e+00 7.43e-01 4.58e+01
  angle pdb=" N   VAL A 477 "
        pdb=" CA  VAL A 477 "
        pdb=" C   VAL A 477 "
      ideal   model   delta    sigma   weight residual
     110.36  115.76   -5.40 1.05e+00 9.07e-01 2.64e+01
  angle pdb=" N   CYS A 125 "
        pdb=" CA  CYS A 125 "
        pdb=" C   CYS A 125 "
      ideal   model   delta    sigma   weight residual
     108.42  116.12   -7.70 1.54e+00 4.22e-01 2.50e+01
  angle pdb=" N   ARG B  59 "
        pdb=" CA  ARG B  59 "
        pdb=" C   ARG B  59 "
      ideal   model   delta    sigma   weight residual
     114.56  108.42    6.14 1.27e+00 6.20e-01 2.34e+01
  angle pdb=" N   SER A 481 "
        pdb=" CA  SER A 481 "
        pdb=" C   SER A 481 "
      ideal   model   delta    sigma   weight residual
     111.07  106.34    4.73 1.07e+00 8.73e-01 1.96e+01
  ... (remaining 14638 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.48: 5923
       23.48 -    46.95: 420
       46.95 -    70.43: 62
       70.43 -    93.91: 12
       93.91 -   117.38: 2
  Dihedral angle restraints: 6419
    sinusoidal: 2471
      harmonic: 3948
  Sorted by residual:
  dihedral pdb=" O2A ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" PB  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   57.38 -117.38     1      2.00e+01 2.50e-03 3.50e+01
  dihedral pdb=" CA  CYS B 223 "
           pdb=" C   CYS B 223 "
           pdb=" N   ASN B 224 "
           pdb=" CA  ASN B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.99   27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   37.46  -97.45     1      2.00e+01 2.50e-03 2.71e+01
  ... (remaining 6416 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1469
       0.073 -    0.146: 184
       0.146 -    0.219: 22
       0.219 -    0.292: 5
       0.292 -    0.365: 1
  Chirality restraints: 1681
  Sorted by residual:
  chirality pdb=" CA  VAL A 558 "
            pdb=" N   VAL A 558 "
            pdb=" C   VAL A 558 "
            pdb=" CB  VAL A 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.08    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CA  HIS B 535 "
            pdb=" N   HIS B 535 "
            pdb=" C   HIS B 535 "
            pdb=" CB  HIS B 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  VAL A 663 "
            pdb=" N   VAL A 663 "
            pdb=" C   VAL A 663 "
            pdb=" CB  VAL A 663 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1678 not shown)

  Planarity restraints: 1892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 242 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   TYR B 242 "    0.056 2.00e-02 2.50e+03
        pdb=" O   TYR B 242 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 243 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 534 "    0.013 2.00e-02 2.50e+03   2.56e-02 6.54e+00
        pdb=" C   VAL B 534 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 534 "    0.016 2.00e-02 2.50e+03
        pdb=" N   HIS B 535 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 724 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 725 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 725 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 725 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1889 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1375
        2.75 -     3.29: 10606
        3.29 -     3.82: 17403
        3.82 -     4.36: 20209
        4.36 -     4.90: 34871
  Nonbonded interactions: 84464
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 223 "
            pdb=" ND1 HIS B 225 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   CYS C 101 "
            pdb=" N   GLY C 104 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" NE2 HIS B 157 "
            pdb=" O   ASN B 608 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   SER B 713 "
            pdb=" OG  SER B 713 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   GLY A 654 "
            pdb=" NH1 ARG C 120 "
     model   vdw
     2.281 3.120
  ... (remaining 84459 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  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:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.920
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5902
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      :  0.010   0.640  10780  Z= 0.469
  Angle     :  0.865  10.839  14643  Z= 0.538
  Chirality :  0.051   0.365   1681
  Planarity :  0.005   0.055   1892
  Dihedral  : 16.072 117.384   3853
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.95 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 16.77 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.21), residues: 1329
  helix: -1.01 (0.18), residues: 692
  sheet: -1.77 (0.52), residues: 92
  loop : -3.41 (0.23), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 308 
 HIS   0.009   0.001   HIS A 540 
 PHE   0.023   0.002   PHE A 634 
 TYR   0.019   0.002   TYR A 507 
 ARG   0.005   0.000   ARG A 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13155 (  499)
  hydrogen bonds       : angle       5.74740 ( 1452)
  metal coordination   : bond        0.32804 (    4)
  covalent geometry    : bond        0.00746 (10776)
  covalent geometry    : angle       0.86451 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 272
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.6916 (t80) cc_final: 0.6557 (t80)
REVERT: A   84 LEU cc_start: 0.8467 (tp) cc_final: 0.8061 (tp)
REVERT: A   93 LEU cc_start: 0.8718 (mt) cc_final: 0.8170 (tt)
REVERT: A  203 LEU cc_start: 0.8736 (tp) cc_final: 0.8425 (tp)
REVERT: A  210 MET cc_start: 0.8690 (mtm) cc_final: 0.8197 (ttm)
REVERT: A  213 THR cc_start: 0.8188 (m) cc_final: 0.7815 (p)
REVERT: A  241 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8679 (m-80)
REVERT: A  249 PHE cc_start: 0.7879 (m-10) cc_final: 0.7323 (m-10)
REVERT: A  271 LEU cc_start: 0.7751 (tt) cc_final: 0.7409 (tt)
REVERT: A  600 MET cc_start: 0.6732 (mmp) cc_final: 0.6011 (tpt)
REVERT: B   49 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6350 (mt)
REVERT: B  143 LEU cc_start: 0.7896 (mt) cc_final: 0.7646 (mt)
REVERT: B  156 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (m)
REVERT: B  601 HIS cc_start: 0.8142 (m-70) cc_final: 0.7790 (m170)
REVERT: B  690 ILE cc_start: 0.7997 (mt) cc_final: 0.7684 (tp)
REVERT: B  748 CYS cc_start: 0.4796 (OUTLIER) cc_final: 0.4148 (t)
REVERT: B  766 TYR cc_start: 0.6760 (t80) cc_final: 0.6452 (t80)
REVERT: C   42 ASP cc_start: 0.6139 (t0) cc_final: 0.5889 (t0)
REVERT: C   63 ASP cc_start: 0.8344 (m-30) cc_final: 0.7710 (m-30)
REVERT: C   77 SER cc_start: 0.8905 (m) cc_final: 0.8335 (p)
REVERT: C   79 LEU cc_start: 0.8452 (mt) cc_final: 0.8160 (tp)
  outliers start: 60
  outliers final: 11
  residues processed: 319
  average time/residue: 0.3087
  time to fit residues: 127.6365
Evaluate side-chains
  171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 54 optimal weight:   20.0000
   chunk 105 optimal weight:    8.9990
   chunk 40 optimal weight:   40.0000
   chunk 64 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 HIS
A 102 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 GLN
A 148 HIS
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
A 377 ASN
A 670 GLN
A 726 HIS
B  68 GLN
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 HIS
B 210 GLN
B 323 GLN
B 491 GLN
B 614 HIS
** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 GLN
C 119 ASN
C 126 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.083846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.068928 restraints weight = 58979.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.070571 restraints weight = 41868.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.071770 restraints weight = 32013.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10780  Z= 0.237
  Angle     :  0.798   9.150  14643  Z= 0.407
  Chirality :  0.045   0.200   1681
  Planarity :  0.006   0.071   1892
  Dihedral  :  6.845 132.477   1501
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.13 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.23), residues: 1329
  helix:  0.02 (0.19), residues: 697
  sheet: -2.00 (0.47), residues: 105
  loop : -2.57 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 308 
 HIS   0.011   0.002   HIS B 617 
 PHE   0.027   0.003   PHE A 241 
 TYR   0.025   0.002   TYR B 123 
 ARG   0.009   0.001   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  499)
  hydrogen bonds       : angle       4.48852 ( 1452)
  metal coordination   : bond        0.00733 (    4)
  covalent geometry    : bond        0.00491 (10776)
  covalent geometry    : angle       0.79755 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 173
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.8956 (p90) cc_final: 0.8626 (p90)
REVERT: A  210 MET cc_start: 0.9189 (mtm) cc_final: 0.8525 (ttm)
REVERT: A  213 THR cc_start: 0.8842 (m) cc_final: 0.8300 (p)
REVERT: A  216 LEU cc_start: 0.8886 (mt) cc_final: 0.8509 (pp)
REVERT: A  249 PHE cc_start: 0.8954 (m-10) cc_final: 0.8271 (m-10)
REVERT: A  299 GLU cc_start: 0.8817 (tp30) cc_final: 0.8503 (tp30)
REVERT: A  335 VAL cc_start: 0.9417 (m) cc_final: 0.8998 (p)
REVERT: A  600 MET cc_start: 0.8756 (mmp) cc_final: 0.8103 (tpt)
REVERT: B   28 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8864 (mm-40)
REVERT: B  232 VAL cc_start: 0.8973 (p) cc_final: 0.8509 (p)
REVERT: B  326 MET cc_start: 0.7013 (tpp) cc_final: 0.6797 (tpt)
REVERT: B  375 MET cc_start: 0.6013 (mmm) cc_final: 0.5662 (mmm)
REVERT: B  419 ASP cc_start: 0.8552 (p0) cc_final: 0.8090 (p0)
REVERT: B  704 GLU cc_start: 0.9247 (pm20) cc_final: 0.8800 (pm20)
REVERT: C   63 ASP cc_start: 0.8423 (m-30) cc_final: 0.7891 (m-30)
  outliers start: 2
  outliers final: 2
  residues processed: 175
  average time/residue: 0.2829
  time to fit residues: 66.5754
Evaluate side-chains
  116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 47 optimal weight:   40.0000
   chunk 83 optimal weight:    5.9990
   chunk 134 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 HIS
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 342 GLN
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.081357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.067166 restraints weight = 60327.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.068732 restraints weight = 42786.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.069862 restraints weight = 32514.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10780  Z= 0.194
  Angle     :  0.738   9.502  14643  Z= 0.371
  Chirality :  0.043   0.158   1681
  Planarity :  0.006   0.046   1892
  Dihedral  :  6.558 140.724   1501
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.94 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.24), residues: 1329
  helix:  0.51 (0.20), residues: 695
  sheet: -1.70 (0.49), residues: 99
  loop : -2.36 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 308 
 HIS   0.014   0.002   HIS A 262 
 PHE   0.022   0.002   PHE A 633 
 TYR   0.016   0.002   TYR B 123 
 ARG   0.014   0.001   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  499)
  hydrogen bonds       : angle       4.29526 ( 1452)
  metal coordination   : bond        0.00424 (    4)
  covalent geometry    : bond        0.00411 (10776)
  covalent geometry    : angle       0.73755 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8232 (mmmt)
REVERT: A  203 LEU cc_start: 0.8969 (tp) cc_final: 0.8519 (tt)
REVERT: A  210 MET cc_start: 0.9112 (mtm) cc_final: 0.8580 (mtt)
REVERT: A  216 LEU cc_start: 0.8735 (mt) cc_final: 0.8532 (pp)
REVERT: A  324 PHE cc_start: 0.6377 (t80) cc_final: 0.6064 (t80)
REVERT: A  335 VAL cc_start: 0.9440 (m) cc_final: 0.9095 (m)
REVERT: A  600 MET cc_start: 0.8780 (mmp) cc_final: 0.8124 (tpt)
REVERT: B  117 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7783 (tp)
REVERT: B  232 VAL cc_start: 0.8882 (p) cc_final: 0.8444 (p)
REVERT: B  419 ASP cc_start: 0.8507 (p0) cc_final: 0.8036 (p0)
REVERT: B  605 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8581 (mt-10)
REVERT: B  704 GLU cc_start: 0.9354 (pm20) cc_final: 0.8930 (pm20)
REVERT: B  737 LEU cc_start: 0.7993 (mt) cc_final: 0.7670 (mt)
REVERT: C   50 MET cc_start: 0.7907 (ttm) cc_final: 0.7037 (mmm)
REVERT: C   63 ASP cc_start: 0.7872 (m-30) cc_final: 0.7192 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 159
  average time/residue: 0.2547
  time to fit residues: 55.8746
Evaluate side-chains
  110 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 127 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 32 optimal weight:   30.0000
   chunk 2 optimal weight:    0.8980
   chunk 118 optimal weight:   20.0000
   chunk 23 optimal weight:    7.9990
   chunk 68 optimal weight:   30.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 617 HIS
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.080954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.066859 restraints weight = 56278.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.068402 restraints weight = 40023.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.069579 restraints weight = 30489.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.5604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10780  Z= 0.164
  Angle     :  0.695   9.495  14643  Z= 0.350
  Chirality :  0.042   0.177   1681
  Planarity :  0.005   0.051   1892
  Dihedral  :  6.389 134.066   1501
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.24), residues: 1329
  helix:  0.74 (0.20), residues: 689
  sheet: -1.55 (0.52), residues: 86
  loop : -2.15 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP A 308 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.014   0.002   PHE A 241 
 TYR   0.013   0.002   TYR B 123 
 ARG   0.011   0.001   ARG B 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (  499)
  hydrogen bonds       : angle       4.20907 ( 1452)
  metal coordination   : bond        0.00211 (    4)
  covalent geometry    : bond        0.00346 (10776)
  covalent geometry    : angle       0.69542 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8039 (mmmt)
REVERT: A  210 MET cc_start: 0.9048 (mtm) cc_final: 0.8480 (ttm)
REVERT: A  226 GLU cc_start: 0.9222 (pm20) cc_final: 0.8974 (pp20)
REVERT: A  266 TRP cc_start: 0.5894 (t60) cc_final: 0.5490 (t60)
REVERT: A  283 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8826 (mmmt)
REVERT: A  299 GLU cc_start: 0.8900 (tp30) cc_final: 0.8649 (tp30)
REVERT: A  324 PHE cc_start: 0.6191 (t80) cc_final: 0.5947 (t80)
REVERT: A  335 VAL cc_start: 0.9382 (m) cc_final: 0.8471 (p)
REVERT: A  352 LEU cc_start: 0.8887 (mt) cc_final: 0.8659 (mt)
REVERT: A  600 MET cc_start: 0.8899 (mmp) cc_final: 0.8020 (tpt)
REVERT: B  155 TYR cc_start: 0.8146 (t80) cc_final: 0.7910 (t80)
REVERT: B  232 VAL cc_start: 0.8495 (p) cc_final: 0.8274 (p)
REVERT: B  419 ASP cc_start: 0.8386 (p0) cc_final: 0.7833 (p0)
REVERT: B  582 MET cc_start: 0.8703 (ttm) cc_final: 0.8385 (ttm)
REVERT: B  605 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8588 (mt-10)
REVERT: B  611 LEU cc_start: 0.9152 (mt) cc_final: 0.8915 (mt)
REVERT: B  704 GLU cc_start: 0.9397 (pm20) cc_final: 0.9003 (pm20)
REVERT: B  737 LEU cc_start: 0.7750 (mt) cc_final: 0.7463 (mt)
REVERT: C   50 MET cc_start: 0.7960 (ttm) cc_final: 0.7101 (mmm)
REVERT: C   63 ASP cc_start: 0.8020 (m-30) cc_final: 0.7433 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2679
  time to fit residues: 54.7448
Evaluate side-chains
  108 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 131 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 HIS
A 597 HIS
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 771 HIS
C  67 ASN
** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.077236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.063615 restraints weight = 59638.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.064984 restraints weight = 42905.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.066088 restraints weight = 33003.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.6395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10780  Z= 0.231
  Angle     :  0.761  11.078  14643  Z= 0.387
  Chirality :  0.044   0.216   1681
  Planarity :  0.006   0.054   1892
  Dihedral  :  6.551 136.616   1501
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 20.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1329
  helix:  0.66 (0.20), residues: 689
  sheet: -1.85 (0.51), residues: 91
  loop : -2.03 (0.28), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 308 
 HIS   0.016   0.002   HIS B 617 
 PHE   0.019   0.002   PHE A 372 
 TYR   0.016   0.002   TYR B 728 
 ARG   0.008   0.001   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03879 (  499)
  hydrogen bonds       : angle       4.44039 ( 1452)
  metal coordination   : bond        0.00549 (    4)
  covalent geometry    : bond        0.00483 (10776)
  covalent geometry    : angle       0.76143 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LEU cc_start: 0.9425 (mt) cc_final: 0.8541 (mt)
REVERT: A  202 GLU cc_start: 0.8532 (tp30) cc_final: 0.8231 (tm-30)
REVERT: A  203 LEU cc_start: 0.8943 (tt) cc_final: 0.8727 (tt)
REVERT: A  210 MET cc_start: 0.9285 (mtm) cc_final: 0.8885 (mtp)
REVERT: A  266 TRP cc_start: 0.6105 (t60) cc_final: 0.5584 (t60)
REVERT: A  299 GLU cc_start: 0.8799 (tp30) cc_final: 0.8573 (tp30)
REVERT: A  324 PHE cc_start: 0.6600 (t80) cc_final: 0.6272 (t80)
REVERT: A  352 LEU cc_start: 0.8838 (mt) cc_final: 0.8575 (mt)
REVERT: A  500 MET cc_start: 0.3956 (mpp) cc_final: 0.3607 (mpp)
REVERT: A  600 MET cc_start: 0.8323 (mmp) cc_final: 0.7568 (tpt)
REVERT: B  155 TYR cc_start: 0.8374 (t80) cc_final: 0.8153 (t80)
REVERT: B  232 VAL cc_start: 0.8360 (p) cc_final: 0.8114 (p)
REVERT: B  326 MET cc_start: 0.7340 (tpt) cc_final: 0.7135 (tpt)
REVERT: B  390 ASP cc_start: 0.9594 (t70) cc_final: 0.9212 (t0)
REVERT: B  419 ASP cc_start: 0.8571 (p0) cc_final: 0.8029 (p0)
REVERT: B  582 MET cc_start: 0.8516 (ttm) cc_final: 0.8206 (ttm)
REVERT: B  605 GLU cc_start: 0.9453 (mt-10) cc_final: 0.8821 (mt-10)
REVERT: B  704 GLU cc_start: 0.9509 (pm20) cc_final: 0.8995 (pm20)
REVERT: B  737 LEU cc_start: 0.7467 (mt) cc_final: 0.7159 (mt)
REVERT: C   50 MET cc_start: 0.8101 (ttm) cc_final: 0.7029 (mmm)
REVERT: C   63 ASP cc_start: 0.8001 (m-30) cc_final: 0.7353 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2244
  time to fit residues: 42.6189
Evaluate side-chains
  106 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 104 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 56 optimal weight:   40.0000
   chunk 2 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 111 optimal weight:    9.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 GLN
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.079444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.065888 restraints weight = 58620.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.067417 restraints weight = 41272.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.068536 restraints weight = 31147.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.6581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10780  Z= 0.151
  Angle     :  0.695   9.942  14643  Z= 0.347
  Chirality :  0.042   0.203   1681
  Planarity :  0.005   0.058   1892
  Dihedral  :  6.330 133.360   1501
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.24), residues: 1329
  helix:  0.86 (0.20), residues: 700
  sheet: -1.55 (0.54), residues: 86
  loop : -1.93 (0.28), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 308 
 HIS   0.008   0.001   HIS B 157 
 PHE   0.022   0.002   PHE A 159 
 TYR   0.017   0.001   TYR A 138 
 ARG   0.006   0.001   ARG B 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  499)
  hydrogen bonds       : angle       4.20825 ( 1452)
  metal coordination   : bond        0.00240 (    4)
  covalent geometry    : bond        0.00318 (10776)
  covalent geometry    : angle       0.69525 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LEU cc_start: 0.9329 (mt) cc_final: 0.8398 (mt)
REVERT: A  202 GLU cc_start: 0.8388 (tp30) cc_final: 0.7880 (tm-30)
REVERT: A  203 LEU cc_start: 0.8878 (tt) cc_final: 0.8585 (tt)
REVERT: A  205 GLN cc_start: 0.8596 (tt0) cc_final: 0.8085 (tt0)
REVERT: A  210 MET cc_start: 0.9293 (mtm) cc_final: 0.8925 (mtp)
REVERT: A  266 TRP cc_start: 0.5838 (t60) cc_final: 0.5490 (t60)
REVERT: A  280 ARG cc_start: 0.6593 (mmm-85) cc_final: 0.5988 (mmm-85)
REVERT: A  299 GLU cc_start: 0.8804 (tp30) cc_final: 0.8533 (tp30)
REVERT: A  324 PHE cc_start: 0.6593 (t80) cc_final: 0.6293 (t80)
REVERT: A  352 LEU cc_start: 0.8847 (mt) cc_final: 0.8585 (mt)
REVERT: A  500 MET cc_start: 0.4087 (mpp) cc_final: 0.3847 (mpp)
REVERT: A  600 MET cc_start: 0.8351 (mmp) cc_final: 0.7668 (tpt)
REVERT: B  155 TYR cc_start: 0.8276 (t80) cc_final: 0.8020 (t80)
REVERT: B  232 VAL cc_start: 0.8548 (p) cc_final: 0.8316 (p)
REVERT: B  390 ASP cc_start: 0.9519 (t70) cc_final: 0.9141 (t0)
REVERT: B  419 ASP cc_start: 0.8559 (p0) cc_final: 0.8058 (p0)
REVERT: B  523 ARG cc_start: 0.9155 (ppt170) cc_final: 0.8815 (ttt-90)
REVERT: B  605 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8583 (mt-10)
REVERT: B  690 ILE cc_start: 0.9479 (pt) cc_final: 0.9114 (tp)
REVERT: B  704 GLU cc_start: 0.9513 (pm20) cc_final: 0.8971 (pm20)
REVERT: B  737 LEU cc_start: 0.7540 (mt) cc_final: 0.7165 (mt)
REVERT: C   50 MET cc_start: 0.7791 (ttm) cc_final: 0.6872 (mmm)
REVERT: C   63 ASP cc_start: 0.7979 (m-30) cc_final: 0.7415 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2533
  time to fit residues: 49.0163
Evaluate side-chains
  106 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 113 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 81 optimal weight:    0.2980
   chunk 52 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 96 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    5.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  72 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
A 646 HIS
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.076267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.062710 restraints weight = 62538.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.064208 restraints weight = 43831.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.065322 restraints weight = 33081.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.7073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10780  Z= 0.219
  Angle     :  0.763  10.180  14643  Z= 0.386
  Chirality :  0.043   0.226   1681
  Planarity :  0.005   0.060   1892
  Dihedral  :  6.442 134.516   1501
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 21.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1329
  helix:  0.58 (0.19), residues: 713
  sheet: -1.67 (0.50), residues: 96
  loop : -2.07 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP A 308 
 HIS   0.013   0.002   HIS B 617 
 PHE   0.027   0.002   PHE A 159 
 TYR   0.013   0.002   TYR A 412 
 ARG   0.007   0.001   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  499)
  hydrogen bonds       : angle       4.46520 ( 1452)
  metal coordination   : bond        0.01021 (    4)
  covalent geometry    : bond        0.00455 (10776)
  covalent geometry    : angle       0.76265 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LEU cc_start: 0.9274 (mt) cc_final: 0.7987 (mt)
REVERT: A  202 GLU cc_start: 0.8658 (tp30) cc_final: 0.8232 (tm-30)
REVERT: A  203 LEU cc_start: 0.8945 (tt) cc_final: 0.8612 (tt)
REVERT: A  210 MET cc_start: 0.9339 (mtm) cc_final: 0.8981 (mtt)
REVERT: A  280 ARG cc_start: 0.6722 (mmm-85) cc_final: 0.6122 (mmm-85)
REVERT: A  299 GLU cc_start: 0.9118 (tp30) cc_final: 0.8676 (tp30)
REVERT: A  324 PHE cc_start: 0.6747 (t80) cc_final: 0.6457 (t80)
REVERT: A  352 LEU cc_start: 0.8574 (mt) cc_final: 0.8310 (mt)
REVERT: A  500 MET cc_start: 0.4531 (mpp) cc_final: 0.4248 (mpp)
REVERT: A  600 MET cc_start: 0.8365 (mmp) cc_final: 0.7748 (tpt)
REVERT: B  155 TYR cc_start: 0.8382 (t80) cc_final: 0.8170 (t80)
REVERT: B  390 ASP cc_start: 0.9558 (t70) cc_final: 0.9270 (t0)
REVERT: B  419 ASP cc_start: 0.8588 (p0) cc_final: 0.8121 (p0)
REVERT: B  605 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8799 (mt-10)
REVERT: B  657 ASP cc_start: 0.8427 (m-30) cc_final: 0.8069 (t0)
REVERT: B  690 ILE cc_start: 0.9431 (pt) cc_final: 0.8979 (tp)
REVERT: B  704 GLU cc_start: 0.9519 (pm20) cc_final: 0.8941 (pm20)
REVERT: B  737 LEU cc_start: 0.7544 (mt) cc_final: 0.7138 (mt)
REVERT: C   60 PRO cc_start: 0.8111 (Cg_endo) cc_final: 0.7835 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2613
  time to fit residues: 47.1148
Evaluate side-chains
  100 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 126 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 115 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0770
   chunk 58 optimal weight:    0.1980
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 ASN
A 375 GLN
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  25 GLN
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.080569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.067278 restraints weight = 58238.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.068772 restraints weight = 41276.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.069874 restraints weight = 31216.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.7044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10780  Z= 0.130
  Angle     :  0.690   9.893  14643  Z= 0.341
  Chirality :  0.042   0.168   1681
  Planarity :  0.004   0.046   1892
  Dihedral  :  6.232 132.136   1501
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.24), residues: 1329
  helix:  0.94 (0.20), residues: 706
  sheet: -1.49 (0.53), residues: 86
  loop : -2.03 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 308 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.020   0.002   PHE A 159 
 TYR   0.016   0.001   TYR C  34 
 ARG   0.004   0.000   ARG B 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  499)
  hydrogen bonds       : angle       4.16066 ( 1452)
  metal coordination   : bond        0.00365 (    4)
  covalent geometry    : bond        0.00281 (10776)
  covalent geometry    : angle       0.68975 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LEU cc_start: 0.9273 (mt) cc_final: 0.8874 (mt)
REVERT: A  202 GLU cc_start: 0.8456 (tp30) cc_final: 0.8024 (tm-30)
REVERT: A  203 LEU cc_start: 0.8902 (tt) cc_final: 0.8495 (tt)
REVERT: A  210 MET cc_start: 0.9177 (mtm) cc_final: 0.8900 (mtp)
REVERT: A  237 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8377 (mt-10)
REVERT: A  280 ARG cc_start: 0.6611 (mmm-85) cc_final: 0.5769 (mmm-85)
REVERT: A  283 LYS cc_start: 0.9258 (mmtm) cc_final: 0.8661 (mmmt)
REVERT: A  299 GLU cc_start: 0.8998 (tp30) cc_final: 0.8743 (tp30)
REVERT: A  324 PHE cc_start: 0.7160 (t80) cc_final: 0.6816 (t80)
REVERT: A  352 LEU cc_start: 0.8939 (mt) cc_final: 0.8723 (mt)
REVERT: A  500 MET cc_start: 0.4280 (mpp) cc_final: 0.3997 (mpp)
REVERT: A  600 MET cc_start: 0.8377 (mmp) cc_final: 0.7755 (tpt)
REVERT: B  155 TYR cc_start: 0.8145 (t80) cc_final: 0.7920 (t80)
REVERT: B  326 MET cc_start: 0.8242 (tpt) cc_final: 0.7557 (tpt)
REVERT: B  419 ASP cc_start: 0.8231 (p0) cc_final: 0.7691 (p0)
REVERT: B  523 ARG cc_start: 0.9209 (ppt170) cc_final: 0.8218 (ttp80)
REVERT: B  605 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8899 (mt-10)
REVERT: B  629 TYR cc_start: 0.8886 (m-10) cc_final: 0.8505 (m-10)
REVERT: B  690 ILE cc_start: 0.9313 (pt) cc_final: 0.8958 (tp)
REVERT: B  695 LEU cc_start: 0.9409 (mm) cc_final: 0.9061 (mm)
REVERT: B  704 GLU cc_start: 0.9389 (pm20) cc_final: 0.8916 (pm20)
REVERT: B  737 LEU cc_start: 0.7445 (mt) cc_final: 0.7017 (mt)
REVERT: B  764 ILE cc_start: 0.9158 (mm) cc_final: 0.8948 (mm)
REVERT: C   50 MET cc_start: 0.6626 (mmm) cc_final: 0.6295 (mmm)
REVERT: C   54 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6812 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2492
  time to fit residues: 49.0955
Evaluate side-chains
  108 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 124 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 120 optimal weight:    6.9990
   chunk 117 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 289 HIS
A 375 GLN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.079228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.065869 restraints weight = 66279.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.067410 restraints weight = 45531.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.068591 restraints weight = 34077.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.7390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10780  Z= 0.175
  Angle     :  0.728  11.649  14643  Z= 0.363
  Chirality :  0.043   0.283   1681
  Planarity :  0.005   0.047   1892
  Dihedral  :  6.268 132.421   1501
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.24), residues: 1329
  helix:  0.95 (0.20), residues: 713
  sheet: -1.68 (0.51), residues: 96
  loop : -1.95 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP A 308 
 HIS   0.010   0.001   HIS B 157 
 PHE   0.031   0.002   PHE B 556 
 TYR   0.014   0.002   TYR A 286 
 ARG   0.007   0.001   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  499)
  hydrogen bonds       : angle       4.21306 ( 1452)
  metal coordination   : bond        0.00701 (    4)
  covalent geometry    : bond        0.00377 (10776)
  covalent geometry    : angle       0.72823 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 GLU cc_start: 0.8731 (tp30) cc_final: 0.8270 (tm-30)
REVERT: A  203 LEU cc_start: 0.8925 (tt) cc_final: 0.8522 (tt)
REVERT: A  210 MET cc_start: 0.9352 (mtm) cc_final: 0.8971 (mtt)
REVERT: A  280 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6202 (mmm-85)
REVERT: A  283 LYS cc_start: 0.9303 (mmtm) cc_final: 0.8836 (mmmt)
REVERT: A  299 GLU cc_start: 0.9207 (tp30) cc_final: 0.8876 (tp30)
REVERT: A  324 PHE cc_start: 0.7368 (t80) cc_final: 0.7069 (t80)
REVERT: A  352 LEU cc_start: 0.8641 (mt) cc_final: 0.8339 (mt)
REVERT: A  500 MET cc_start: 0.4685 (mpp) cc_final: 0.4411 (mpp)
REVERT: A  600 MET cc_start: 0.8367 (mmp) cc_final: 0.7812 (tpt)
REVERT: B  155 TYR cc_start: 0.8350 (t80) cc_final: 0.8090 (t80)
REVERT: B  419 ASP cc_start: 0.8299 (p0) cc_final: 0.7787 (p0)
REVERT: B  523 ARG cc_start: 0.9210 (ppt170) cc_final: 0.8810 (ttt-90)
REVERT: B  605 GLU cc_start: 0.9478 (mt-10) cc_final: 0.8964 (mt-10)
REVERT: B  629 TYR cc_start: 0.8841 (m-10) cc_final: 0.8437 (m-10)
REVERT: B  690 ILE cc_start: 0.9425 (pt) cc_final: 0.9018 (tp)
REVERT: B  695 LEU cc_start: 0.9460 (mm) cc_final: 0.9161 (mm)
REVERT: B  704 GLU cc_start: 0.9575 (pm20) cc_final: 0.8961 (pm20)
REVERT: B  734 ASP cc_start: 0.8978 (m-30) cc_final: 0.8592 (t0)
REVERT: B  737 LEU cc_start: 0.7522 (mt) cc_final: 0.7185 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2382
  time to fit residues: 43.3314
Evaluate side-chains
  102 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 103 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0570
   chunk 79 optimal weight:    0.0470
   chunk 88 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 94 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    3.2202

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.078991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.065534 restraints weight = 60162.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.067080 restraints weight = 42454.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.068147 restraints weight = 32118.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.7533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10780  Z= 0.154
  Angle     :  0.719  12.142  14643  Z= 0.355
  Chirality :  0.043   0.268   1681
  Planarity :  0.005   0.049   1892
  Dihedral  :  6.263 131.948   1501
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.24), residues: 1329
  helix:  1.00 (0.20), residues: 710
  sheet: -1.64 (0.53), residues: 86
  loop : -1.97 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP A 308 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.041   0.002   PHE A 241 
 TYR   0.009   0.001   TYR A 507 
 ARG   0.006   0.000   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03400 (  499)
  hydrogen bonds       : angle       4.19216 ( 1452)
  metal coordination   : bond        0.00442 (    4)
  covalent geometry    : bond        0.00338 (10776)
  covalent geometry    : angle       0.71921 (14643)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 GLU cc_start: 0.8669 (tp30) cc_final: 0.8246 (tm-30)
REVERT: A  203 LEU cc_start: 0.8943 (tt) cc_final: 0.8510 (tt)
REVERT: A  210 MET cc_start: 0.9319 (mtm) cc_final: 0.9097 (mtp)
REVERT: A  267 PHE cc_start: 0.7590 (t80) cc_final: 0.7243 (t80)
REVERT: A  280 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6198 (mmm-85)
REVERT: A  283 LYS cc_start: 0.9273 (mmtm) cc_final: 0.8783 (mmmt)
REVERT: A  299 GLU cc_start: 0.9177 (tp30) cc_final: 0.8891 (tp30)
REVERT: A  324 PHE cc_start: 0.7321 (t80) cc_final: 0.7022 (t80)
REVERT: A  328 ASP cc_start: 0.8200 (p0) cc_final: 0.7845 (p0)
REVERT: A  352 LEU cc_start: 0.8642 (mt) cc_final: 0.8270 (mt)
REVERT: A  370 MET cc_start: 0.7433 (mmp) cc_final: 0.7131 (mmm)
REVERT: A  500 MET cc_start: 0.4630 (mpp) cc_final: 0.4387 (mpp)
REVERT: A  600 MET cc_start: 0.8413 (mmp) cc_final: 0.7759 (tpt)
REVERT: B  155 TYR cc_start: 0.8233 (t80) cc_final: 0.7964 (t80)
REVERT: B  326 MET cc_start: 0.7315 (tpt) cc_final: 0.7054 (tpt)
REVERT: B  329 PHE cc_start: 0.8864 (t80) cc_final: 0.8541 (t80)
REVERT: B  419 ASP cc_start: 0.8239 (p0) cc_final: 0.7657 (p0)
REVERT: B  523 ARG cc_start: 0.9213 (ppt170) cc_final: 0.8795 (ttt-90)
REVERT: B  605 GLU cc_start: 0.9475 (mt-10) cc_final: 0.8947 (mt-10)
REVERT: B  629 TYR cc_start: 0.8830 (m-10) cc_final: 0.8428 (m-10)
REVERT: B  690 ILE cc_start: 0.9423 (pt) cc_final: 0.9015 (tp)
REVERT: B  695 LEU cc_start: 0.9455 (mm) cc_final: 0.9199 (mm)
REVERT: B  704 GLU cc_start: 0.9389 (pm20) cc_final: 0.8904 (pm20)
REVERT: B  734 ASP cc_start: 0.8960 (m-30) cc_final: 0.8574 (t0)
REVERT: B  737 LEU cc_start: 0.7456 (mt) cc_final: 0.7130 (mt)
REVERT: B  738 VAL cc_start: 0.7519 (t) cc_final: 0.7284 (t)
REVERT: B  764 ILE cc_start: 0.9164 (mm) cc_final: 0.8945 (mm)
REVERT: C   50 MET cc_start: 0.7095 (mmt) cc_final: 0.6133 (mmp)
REVERT: C   54 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6972 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2471
  time to fit residues: 43.8846
Evaluate side-chains
  103 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 127 optimal weight:   20.0000
   chunk 101 optimal weight:    0.9980
   chunk 122 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  25 GLN
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.077802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.064697 restraints weight = 65070.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.066253 restraints weight = 44921.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.067297 restraints weight = 33573.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.7861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10780  Z= 0.204
  Angle     :  0.756  10.903  14643  Z= 0.380
  Chirality :  0.043   0.246   1681
  Planarity :  0.005   0.053   1892
  Dihedral  :  6.382 132.144   1501
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.24), residues: 1329
  helix:  0.75 (0.20), residues: 725
  sheet: -1.83 (0.51), residues: 96
  loop : -2.08 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP A 308 
 HIS   0.011   0.002   HIS B 157 
 PHE   0.040   0.002   PHE A 241 
 TYR   0.021   0.002   TYR A 138 
 ARG   0.006   0.001   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  499)
  hydrogen bonds       : angle       4.38007 ( 1452)
  metal coordination   : bond        0.00372 (    4)
  covalent geometry    : bond        0.00431 (10776)
  covalent geometry    : angle       0.75559 (14643)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.46 seconds
wall clock time: 53 minutes 5.97 seconds (3185.97 seconds total)