Starting phenix.real_space_refine
on Fri Mar 14 01:03:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vk0_21222/03_2025/6vk0_21222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vk0_21222/03_2025/6vk0_21222.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2025/6vk0_21222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2025/6vk0_21222.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2025/6vk0_21222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2025/6vk0_21222.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6267      2.51       5
     N    1561      2.21       5
     O    1687      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9559
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 823
          Classifications: {'peptide': 97}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 89}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1470
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 4923
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 20, 'TRANS': 582}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2343
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 5.52, per 1000 atoms: 0.58
  Number of scatterers: 9559
  At special positions: 0
  Unit cell: (110.7, 99.9, 148.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1687      8.00
     N    1561      7.00
     C    6267      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2230

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      79.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'D' and resid 535 through 544
      removed outlier: 3.800A  pdb=" N   VAL D 539 " --> pdb=" O   PRO D 535 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LEU D 540 " --> pdb=" O   LEU D 536 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 549 through 551
      No H-bonds generated for 'chain 'D' and resid 549 through 551'
    Processing helix  chain 'D' and resid 552 through 562
      removed outlier: 4.358A  pdb=" N   PHE D 556 " --> pdb=" O   LEU D 552 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ILE D 557 " --> pdb=" O   VAL D 553 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE D 558 " --> pdb=" O   PRO D 554 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 563 through 565
      No H-bonds generated for 'chain 'D' and resid 563 through 565'
    Processing helix  chain 'D' and resid 566 through 567
      No H-bonds generated for 'chain 'D' and resid 566 through 567'
    Processing helix  chain 'D' and resid 568 through 581
      removed outlier: 3.853A  pdb=" N   THR D 581 " --> pdb=" O   PHE D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 753
    Processing helix  chain 'D' and resid 763 through 778
      removed outlier: 3.522A  pdb=" N   VAL D 777 " --> pdb=" O   VAL D 773 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 789
      removed outlier: 4.103A  pdb=" N   LYS D 786 " --> pdb=" O   TYR D 782 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 32
    Processing helix  chain 'C' and resid 43 through 51
      removed outlier: 3.537A  pdb=" N   VAL C  47 " --> pdb=" O   SER C  43 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS C  49 " --> pdb=" O   ASP C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 58
      removed outlier: 3.806A  pdb=" N   LEU C  57 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 61
      No H-bonds generated for 'chain 'C' and resid 59 through 61'
    Processing helix  chain 'C' and resid 67 through 85
    Processing helix  chain 'C' and resid 86 through 88
      No H-bonds generated for 'chain 'C' and resid 86 through 88'
    Processing helix  chain 'C' and resid 92 through 110
      removed outlier: 3.741A  pdb=" N   TRP C  96 " --> pdb=" O   ARG C  92 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE C  99 " --> pdb=" O   CYS C  95 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU C 100 " --> pdb=" O   TRP C  96 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   VAL C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   MET C 108 " --> pdb=" O   ILE C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 134
    Processing helix  chain 'C' and resid 152 through 165
      removed outlier: 3.805A  pdb=" N   TYR C 156 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 174
    Processing helix  chain 'C' and resid 176 through 192
      removed outlier: 4.126A  pdb=" N   ILE C 189 " --> pdb=" O   MET C 185 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLY C 190 " --> pdb=" O   ASP C 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 35
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.579A  pdb=" N   GLU A  46 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.591A  pdb=" N   HIS A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.608A  pdb=" N   ILE A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY A 156 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 185
      removed outlier: 3.734A  pdb=" N   GLY A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 197
    Processing helix  chain 'A' and resid 206 through 225
      removed outlier: 3.785A  pdb=" N   SER A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
      removed outlier: 3.514A  pdb=" N   ASP A 231 " --> pdb=" O   ARG A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 329
      removed outlier: 3.694A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 4.186A  pdb=" N   ALA A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.576A  pdb=" N   ASN A 360 " --> pdb=" O   HIS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.895A  pdb=" N   TYR A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.867A  pdb=" N   ARG A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 410
      No H-bonds generated for 'chain 'A' and resid 408 through 410'
    Processing helix  chain 'A' and resid 412 through 426
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.982A  pdb=" N   ALA A 433 " --> pdb=" O   ASN A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
      removed outlier: 4.005A  pdb=" N   LYS A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 462 through 465'
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.699A  pdb=" N   ILE A 485 " --> pdb=" O   PHE A 481 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY A 495 " --> pdb=" O   MET A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 4.228A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.696A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 550
      removed outlier: 3.933A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLN A 549 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY A 550 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.590A  pdb=" N   LYS A 580 " --> pdb=" O   THR A 576 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 610
      removed outlier: 3.842A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 624
      removed outlier: 4.414A  pdb=" N   ALA A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.827A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 685
      removed outlier: 3.724A  pdb=" N   ILE A 685 " --> pdb=" O   TRP A 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 31
    Processing helix  chain 'B' and resid 34 through 43
      removed outlier: 3.729A  pdb=" N   ASN B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 71
    Processing helix  chain 'B' and resid 75 through 99
      Proline residue:  B  87  - end of helix
      removed outlier: 3.544A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 104
    Processing helix  chain 'B' and resid 105 through 135
      removed outlier: 4.162A  pdb=" N   ALA B 109 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 175
    Processing helix  chain 'B' and resid 179 through 220
      removed outlier: 3.658A  pdb=" N   THR B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 294
      removed outlier: 4.252A  pdb=" N   TYR B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      Proline residue:  B 292  - end of helix
    Processing helix  chain 'B' and resid 297 through 324

    616 hydrogen bonds defined for protein.
    1842 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2932
        1.34 -     1.46: 2414
        1.46 -     1.58: 4379
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 9804
  Sorted by residual:
  bond pdb=" N   LYS D 568 "
       pdb=" CA  LYS D 568 "
    ideal  model  delta    sigma   weight residual
    1.457  1.419  0.038 1.35e-02 5.49e+03 8.13e+00
  bond pdb=" N   SER B 135 "
       pdb=" CA  SER B 135 "
    ideal  model  delta    sigma   weight residual
    1.457  1.425  0.032 1.40e-02 5.10e+03 5.19e+00
  bond pdb=" CA  GLN B 134 "
       pdb=" C   GLN B 134 "
    ideal  model  delta    sigma   weight residual
    1.524  1.553 -0.029 1.29e-02 6.01e+03 4.98e+00
  bond pdb=" CA  SER A 262 "
       pdb=" CB  SER A 262 "
    ideal  model  delta    sigma   weight residual
    1.531  1.470  0.061 3.28e-02 9.30e+02 3.46e+00
  bond pdb=" CA  LEU D 565 "
       pdb=" C   LEU D 565 "
    ideal  model  delta    sigma   weight residual
    1.532  1.520  0.012 6.50e-03 2.37e+04 3.42e+00
  ... (remaining 9799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 12933
        2.23 -     4.47: 305
        4.47 -     6.70: 42
        6.70 -     8.94: 5
        8.94 -    11.17: 2
  Bond angle restraints: 13287
  Sorted by residual:
  angle pdb=" N   ASP A 246 "
        pdb=" CA  ASP A 246 "
        pdb=" C   ASP A 246 "
      ideal   model   delta    sigma   weight residual
     113.38  102.21   11.17 1.23e+00 6.61e-01 8.25e+01
  angle pdb=" N   GLY A 253 "
        pdb=" CA  GLY A 253 "
        pdb=" C   GLY A 253 "
      ideal   model   delta    sigma   weight residual
     112.48  118.48   -6.00 1.21e+00 6.83e-01 2.46e+01
  angle pdb=" N   MET C 138 "
        pdb=" CA  MET C 138 "
        pdb=" C   MET C 138 "
      ideal   model   delta    sigma   weight residual
     110.68  104.35    6.33 1.39e+00 5.18e-01 2.07e+01
  angle pdb=" N   THR B 194 "
        pdb=" CA  THR B 194 "
        pdb=" CB  THR B 194 "
      ideal   model   delta    sigma   weight residual
     110.07  116.23   -6.16 1.45e+00 4.76e-01 1.80e+01
  angle pdb=" C   PHE D 564 "
        pdb=" N   LEU D 565 "
        pdb=" CA  LEU D 565 "
      ideal   model   delta    sigma   weight residual
     123.10  126.46   -3.36 9.60e-01 1.09e+00 1.22e+01
  ... (remaining 13282 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 5122
       17.87 -    35.74: 525
       35.74 -    53.61: 108
       53.61 -    71.48: 12
       71.48 -    89.35: 5
  Dihedral angle restraints: 5772
    sinusoidal: 2318
      harmonic: 3454
  Sorted by residual:
  dihedral pdb=" CA  TRP D 567 "
           pdb=" C   TRP D 567 "
           pdb=" N   LYS D 568 "
           pdb=" CA  LYS D 568 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.44   24.56     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  GLU A 104 "
           pdb=" C   GLU A 104 "
           pdb=" N   ALA A 105 "
           pdb=" CA  ALA A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.80   23.20     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  VAL C 103 "
           pdb=" C   VAL C 103 "
           pdb=" N   ILE C 104 "
           pdb=" CA  ILE C 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.02  -22.98     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 5769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1276
       0.068 -    0.137: 186
       0.137 -    0.205: 12
       0.205 -    0.273: 2
       0.273 -    0.341: 2
  Chirality restraints: 1478
  Sorted by residual:
  chirality pdb=" CA  LEU A 252 "
            pdb=" N   LEU A 252 "
            pdb=" C   LEU A 252 "
            pdb=" CB  LEU A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CA  SER A 245 "
            pdb=" N   SER A 245 "
            pdb=" C   SER A 245 "
            pdb=" CB  SER A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CB  ILE A  37 "
            pdb=" CA  ILE A  37 "
            pdb=" CG1 ILE A  37 "
            pdb=" CG2 ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1475 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B   2 "    0.035 5.00e-02 4.00e+02   5.25e-02 4.40e+00
        pdb=" N   PRO B   3 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B   3 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B   3 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 244 "   -0.011 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   ILE A 244 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE A 244 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 245 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  27 "   -0.033 5.00e-02 4.00e+02   4.92e-02 3.88e+00
        pdb=" N   PRO A  28 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1358
        2.74 -     3.28: 10666
        3.28 -     3.82: 15460
        3.82 -     4.36: 17351
        4.36 -     4.90: 28036
  Nonbonded interactions: 72871
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 758 "
            pdb=" ND2 ASN D 761 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" NE2 GLN A 424 "
            pdb=" OE1 GLN A 453 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" ND2 ASN A 595 "
            pdb=" OD1 ASP A 597 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OG  SER A  97 "
            pdb=" OG1 THR A 106 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLN A 432 "
            pdb=" OG  SER A 435 "
     model   vdw
     2.227 3.040
  ... (remaining 72866 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:             0.230
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.350
  Find NCS groups from input model:        0.080
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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      :  0.007   0.061   9804  Z= 0.446
  Angle     :  0.844  11.174  13287  Z= 0.493
  Chirality :  0.049   0.341   1478
  Planarity :  0.005   0.052   1642
  Dihedral  : 14.838  89.349   3542
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 10.53 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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: -3.49 (0.20), residues: 1140
  helix: -1.94 (0.14), residues: 797
  sheet:  None (None), residues: 0
  loop : -2.83 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 684 
 HIS   0.011   0.002   HIS B 286 
 PHE   0.033   0.002   PHE B  88 
 TYR   0.029   0.002   TYR B  18 
 ARG   0.009   0.001   ARG A 265 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 320
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7063 (pttp)
REVERT: C   52 GLN cc_start: 0.6224 (tp-100) cc_final: 0.5328 (pm20)
REVERT: C   91 ARG cc_start: 0.7374 (mpt180) cc_final: 0.6747 (mtt-85)
REVERT: C   99 PHE cc_start: 0.7147 (m-80) cc_final: 0.6472 (m-80)
REVERT: C  125 ASN cc_start: 0.8683 (m110) cc_final: 0.8417 (m110)
REVERT: C  130 GLU cc_start: 0.8178 (tp30) cc_final: 0.7971 (tp30)
REVERT: C  137 GLN cc_start: 0.8181 (mt0) cc_final: 0.7697 (mt0)
REVERT: C  166 LYS cc_start: 0.8312 (tppt) cc_final: 0.7994 (tptp)
REVERT: C  189 ILE cc_start: 0.5628 (tt) cc_final: 0.5381 (tp)
REVERT: C  191 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7708 (tmtt)
REVERT: A   49 MET cc_start: 0.8227 (mmm) cc_final: 0.7857 (mmt)
REVERT: A   74 TYR cc_start: 0.8360 (t80) cc_final: 0.7932 (t80)
REVERT: A   90 TYR cc_start: 0.7917 (t80) cc_final: 0.7485 (t80)
REVERT: A   93 LEU cc_start: 0.9416 (mm) cc_final: 0.9082 (mm)
REVERT: A  180 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7712 (tpp-160)
REVERT: A  256 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8111 (tp)
REVERT: A  438 MET cc_start: 0.7660 (mmm) cc_final: 0.6753 (mmm)
REVERT: A  439 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7737 (mtpt)
REVERT: A  461 PHE cc_start: 0.8370 (m-80) cc_final: 0.7882 (m-80)
REVERT: A  520 MET cc_start: 0.8918 (mmm) cc_final: 0.8649 (mmm)
REVERT: A  537 GLU cc_start: 0.7733 (tp30) cc_final: 0.7214 (tp30)
REVERT: A  614 LYS cc_start: 0.8568 (tttt) cc_final: 0.8083 (mttt)
REVERT: B  168 CYS cc_start: 0.8976 (m) cc_final: 0.8264 (t)
REVERT: B  186 TYR cc_start: 0.8537 (m-10) cc_final: 0.8265 (m-80)
REVERT: B  195 MET cc_start: 0.9083 (mtp) cc_final: 0.8840 (mtm)
  outliers start: 2
  outliers final: 1
  residues processed: 322
  average time/residue: 0.2272
  time to fit residues: 99.1957
Evaluate side-chains
  251 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 249
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 87 optimal weight:    0.0670
   chunk 48 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    9.9990
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
D 745 HIS
D 771 ASN
** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
A  86 GLN
A 202 ASN
A 429 ASN
A 504 ASN
A 593 GLN
A 595 ASN
A 661 HIS
B  79 HIS
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.156744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.125794 restraints weight = 21232.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.125087 restraints weight = 14042.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.126090 restraints weight = 11846.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9804  Z= 0.200
  Angle     :  0.673  12.298  13287  Z= 0.353
  Chirality :  0.042   0.164   1478
  Planarity :  0.005   0.083   1642
  Dihedral  :  5.453  26.955   1277
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.17 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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: -1.01 (0.24), residues: 1140
  helix: -0.05 (0.17), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.15 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C  19 
 HIS   0.013   0.001   HIS B  79 
 PHE   0.037   0.002   PHE C  75 
 TYR   0.022   0.002   TYR C  42 
 ARG   0.012   0.001   ARG C  55 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 343
  time to evaluate  : 1.104 
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: D  770 LYS cc_start: 0.7423 (mmtt) cc_final: 0.6314 (pttp)
REVERT: C   39 LYS cc_start: 0.5766 (mttt) cc_final: 0.5188 (mmtt)
REVERT: C   75 PHE cc_start: 0.7729 (m-80) cc_final: 0.6983 (m-80)
REVERT: C   91 ARG cc_start: 0.7181 (mpt180) cc_final: 0.6681 (mtt180)
REVERT: C   99 PHE cc_start: 0.6450 (m-80) cc_final: 0.5899 (m-80)
REVERT: C  112 GLU cc_start: 0.6650 (pm20) cc_final: 0.5276 (tm-30)
REVERT: C  130 GLU cc_start: 0.7852 (tp30) cc_final: 0.7643 (tp30)
REVERT: C  137 GLN cc_start: 0.8069 (mt0) cc_final: 0.7732 (mt0)
REVERT: A   49 MET cc_start: 0.8334 (mmm) cc_final: 0.7608 (mmt)
REVERT: A   79 GLN cc_start: 0.7975 (mm110) cc_final: 0.7702 (mm110)
REVERT: A   93 LEU cc_start: 0.9509 (mm) cc_final: 0.9296 (mm)
REVERT: A  132 GLU cc_start: 0.7469 (tp30) cc_final: 0.7115 (tp30)
REVERT: A  336 GLN cc_start: 0.8759 (tt0) cc_final: 0.8308 (tt0)
REVERT: A  372 CYS cc_start: 0.9036 (m) cc_final: 0.8628 (m)
REVERT: A  438 MET cc_start: 0.7775 (mmm) cc_final: 0.7530 (mmt)
REVERT: A  453 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8603 (mm-40)
REVERT: A  461 PHE cc_start: 0.8121 (m-80) cc_final: 0.7819 (m-10)
REVERT: A  478 LEU cc_start: 0.9303 (mt) cc_final: 0.9100 (mt)
REVERT: A  520 MET cc_start: 0.8828 (mmm) cc_final: 0.8463 (mmm)
REVERT: A  614 LYS cc_start: 0.8308 (tttt) cc_final: 0.7932 (mttp)
REVERT: A  639 GLU cc_start: 0.8670 (pp20) cc_final: 0.8189 (pp20)
REVERT: A  642 LEU cc_start: 0.7778 (pp) cc_final: 0.6828 (pp)
REVERT: A  676 LEU cc_start: 0.7833 (tp) cc_final: 0.7510 (tp)
REVERT: A  679 LYS cc_start: 0.8347 (mttt) cc_final: 0.8097 (mtpp)
REVERT: B    4 GLU cc_start: 0.7093 (pm20) cc_final: 0.6503 (tm-30)
REVERT: B   36 LEU cc_start: 0.8726 (tp) cc_final: 0.8108 (mm)
REVERT: B   76 LEU cc_start: 0.8642 (mt) cc_final: 0.8374 (mt)
REVERT: B   80 GLU cc_start: 0.8936 (mp0) cc_final: 0.8653 (mp0)
REVERT: B   81 HIS cc_start: 0.8909 (m-70) cc_final: 0.8107 (m-70)
REVERT: B   95 PHE cc_start: 0.7477 (t80) cc_final: 0.7238 (t80)
REVERT: B  142 MET cc_start: 0.6770 (tpp) cc_final: 0.6474 (tpp)
REVERT: B  192 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8628 (mm-30)
REVERT: B  195 MET cc_start: 0.8958 (mtp) cc_final: 0.8741 (mtm)
REVERT: B  203 LEU cc_start: 0.8783 (mm) cc_final: 0.8576 (mm)
REVERT: B  289 MET cc_start: 0.6556 (ttt) cc_final: 0.5491 (mmt)
  outliers start: 3
  outliers final: 1
  residues processed: 344
  average time/residue: 0.1922
  time to fit residues: 94.7525
Evaluate side-chains
  264 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
C 175 ASN
A 117 GLN
A 123 ASN
A 135 ASN
B 189 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.157332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126444 restraints weight = 21720.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.128233 restraints weight = 12241.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.129084 restraints weight = 9795.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9804  Z= 0.206
  Angle     :  0.636  11.104  13287  Z= 0.333
  Chirality :  0.042   0.203   1478
  Planarity :  0.004   0.057   1642
  Dihedral  :  5.195  26.753   1277
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.35 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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: -0.16 (0.25), residues: 1140
  helix:  0.57 (0.18), residues: 840
  sheet:  None (None), residues: 0
  loop : -1.93 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  27 
 HIS   0.005   0.001   HIS A 640 
 PHE   0.025   0.002   PHE C  75 
 TYR   0.019   0.002   TYR B 117 
 ARG   0.005   0.000   ARG C  55 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 329
  time to evaluate  : 1.104 
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: D  770 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7199 (pttp)
REVERT: C   39 LYS cc_start: 0.5891 (mttt) cc_final: 0.5323 (mmtt)
REVERT: C   71 MET cc_start: 0.8410 (tpt) cc_final: 0.7951 (tpt)
REVERT: C   75 PHE cc_start: 0.7801 (m-80) cc_final: 0.7111 (m-80)
REVERT: C   99 PHE cc_start: 0.6393 (m-80) cc_final: 0.5834 (m-80)
REVERT: C  109 THR cc_start: 0.7777 (t) cc_final: 0.7054 (t)
REVERT: C  112 GLU cc_start: 0.7657 (pm20) cc_final: 0.5203 (tm-30)
REVERT: C  120 VAL cc_start: 0.8405 (t) cc_final: 0.7222 (t)
REVERT: C  121 LEU cc_start: 0.9429 (mt) cc_final: 0.9145 (mt)
REVERT: C  130 GLU cc_start: 0.7948 (tp30) cc_final: 0.7679 (tp30)
REVERT: C  137 GLN cc_start: 0.7846 (mt0) cc_final: 0.7596 (tt0)
REVERT: A   49 MET cc_start: 0.8145 (mmm) cc_final: 0.7491 (mmt)
REVERT: A   79 GLN cc_start: 0.8056 (mm110) cc_final: 0.7720 (mm110)
REVERT: A   93 LEU cc_start: 0.9480 (mm) cc_final: 0.9171 (mm)
REVERT: A  336 GLN cc_start: 0.8731 (tt0) cc_final: 0.8267 (tt0)
REVERT: A  372 CYS cc_start: 0.9043 (m) cc_final: 0.8628 (m)
REVERT: A  520 MET cc_start: 0.8835 (mmm) cc_final: 0.8499 (mmm)
REVERT: A  534 ASP cc_start: 0.8468 (t70) cc_final: 0.8139 (t70)
REVERT: A  614 LYS cc_start: 0.8322 (tttt) cc_final: 0.7817 (mttp)
REVERT: B    4 GLU cc_start: 0.7122 (pm20) cc_final: 0.6602 (tm-30)
REVERT: B   36 LEU cc_start: 0.8823 (tp) cc_final: 0.8208 (mm)
REVERT: B   81 HIS cc_start: 0.8831 (m-70) cc_final: 0.7945 (m90)
REVERT: B  142 MET cc_start: 0.6755 (tpp) cc_final: 0.6328 (tpp)
REVERT: B  191 MET cc_start: 0.8528 (tmm) cc_final: 0.8097 (tmm)
REVERT: B  192 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8617 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 329
  average time/residue: 0.1774
  time to fit residues: 85.3562
Evaluate side-chains
  259 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
C 175 ASN
A  88 HIS
A 113 HIS
A 123 ASN
B  79 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.157579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.127616 restraints weight = 21702.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127479 restraints weight = 15072.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128481 restraints weight = 12670.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9804  Z= 0.198
  Angle     :  0.632  11.129  13287  Z= 0.325
  Chirality :  0.041   0.163   1478
  Planarity :  0.004   0.056   1642
  Dihedral  :  5.007  24.068   1277
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.73 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.26 (0.25), residues: 1140
  helix:  0.90 (0.18), residues: 835
  sheet:  None (None), residues: 0
  loop : -1.83 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  27 
 HIS   0.009   0.001   HIS B  79 
 PHE   0.024   0.002   PHE C  88 
 TYR   0.023   0.001   TYR B 117 
 ARG   0.003   0.000   ARG C 141 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 322
  time to evaluate  : 1.030 
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: D  770 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7107 (pttp)
REVERT: C   39 LYS cc_start: 0.5947 (mttt) cc_final: 0.5421 (mmtt)
REVERT: C   71 MET cc_start: 0.8204 (tpt) cc_final: 0.7718 (tpt)
REVERT: C   75 PHE cc_start: 0.7824 (m-80) cc_final: 0.7251 (m-80)
REVERT: C   91 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6958 (mtt180)
REVERT: C   99 PHE cc_start: 0.6293 (m-80) cc_final: 0.5876 (m-80)
REVERT: C  120 VAL cc_start: 0.8487 (t) cc_final: 0.7213 (t)
REVERT: C  121 LEU cc_start: 0.9500 (mt) cc_final: 0.9277 (mt)
REVERT: C  122 LEU cc_start: 0.9414 (mm) cc_final: 0.9196 (mm)
REVERT: C  137 GLN cc_start: 0.7753 (mt0) cc_final: 0.7453 (mt0)
REVERT: C  177 MET cc_start: 0.8467 (mmm) cc_final: 0.8098 (mmm)
REVERT: A   49 MET cc_start: 0.8114 (mmm) cc_final: 0.7529 (mmt)
REVERT: A   79 GLN cc_start: 0.8139 (mm110) cc_final: 0.7814 (mm110)
REVERT: A   93 LEU cc_start: 0.9449 (mm) cc_final: 0.9123 (mm)
REVERT: A  132 GLU cc_start: 0.8028 (tp30) cc_final: 0.7602 (tp30)
REVERT: A  246 ASP cc_start: 0.8763 (m-30) cc_final: 0.7791 (t0)
REVERT: A  372 CYS cc_start: 0.9043 (m) cc_final: 0.8673 (m)
REVERT: A  520 MET cc_start: 0.8790 (mmm) cc_final: 0.8211 (mmm)
REVERT: A  534 ASP cc_start: 0.8427 (t70) cc_final: 0.8079 (t70)
REVERT: A  614 LYS cc_start: 0.8317 (tttt) cc_final: 0.7772 (mttp)
REVERT: A  652 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8257 (tttt)
REVERT: B    4 GLU cc_start: 0.7098 (pm20) cc_final: 0.6663 (tm-30)
REVERT: B   36 LEU cc_start: 0.8739 (tp) cc_final: 0.8128 (mm)
REVERT: B   95 PHE cc_start: 0.7744 (t80) cc_final: 0.7161 (t80)
REVERT: B  142 MET cc_start: 0.6574 (tpp) cc_final: 0.6198 (tpp)
REVERT: B  168 CYS cc_start: 0.9180 (m) cc_final: 0.8908 (m)
REVERT: B  195 MET cc_start: 0.8924 (mtm) cc_final: 0.8714 (mtm)
REVERT: B  204 PHE cc_start: 0.8223 (t80) cc_final: 0.7871 (t80)
REVERT: B  289 MET cc_start: 0.5773 (ttt) cc_final: 0.5489 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 322
  average time/residue: 0.1712
  time to fit residues: 81.1985
Evaluate side-chains
  262 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 63 optimal weight:    8.9990
   chunk 56 optimal weight:    0.2980
   chunk 17 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.160200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130694 restraints weight = 21698.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.130238 restraints weight = 14451.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131162 restraints weight = 11832.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9804  Z= 0.169
  Angle     :  0.622  10.936  13287  Z= 0.319
  Chirality :  0.040   0.195   1478
  Planarity :  0.004   0.048   1642
  Dihedral  :  4.840  23.072   1277
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.20 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.35 (0.25), residues: 1140
  helix:  1.02 (0.18), residues: 849
  sheet:  None (None), residues: 0
  loop : -2.08 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  27 
 HIS   0.005   0.001   HIS B 122 
 PHE   0.019   0.001   PHE D 544 
 TYR   0.030   0.001   TYR A 380 
 ARG   0.002   0.000   ARG C  55 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 318
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7113 (pttp)
REVERT: C   71 MET cc_start: 0.8168 (tpt) cc_final: 0.7793 (tpt)
REVERT: C   75 PHE cc_start: 0.7746 (m-80) cc_final: 0.7302 (m-80)
REVERT: C   99 PHE cc_start: 0.6002 (m-80) cc_final: 0.5640 (m-80)
REVERT: C  109 THR cc_start: 0.7717 (t) cc_final: 0.7192 (t)
REVERT: C  112 GLU cc_start: 0.7788 (pm20) cc_final: 0.5399 (tm-30)
REVERT: C  120 VAL cc_start: 0.8329 (t) cc_final: 0.7175 (t)
REVERT: C  121 LEU cc_start: 0.9479 (mt) cc_final: 0.9189 (mt)
REVERT: C  122 LEU cc_start: 0.9348 (mm) cc_final: 0.9135 (mm)
REVERT: C  137 GLN cc_start: 0.7655 (mt0) cc_final: 0.7310 (mt0)
REVERT: C  177 MET cc_start: 0.8542 (mmm) cc_final: 0.8090 (mmm)
REVERT: A   49 MET cc_start: 0.8034 (mmm) cc_final: 0.7788 (mmt)
REVERT: A   74 TYR cc_start: 0.7810 (t80) cc_final: 0.7106 (t80)
REVERT: A   79 GLN cc_start: 0.8178 (mm110) cc_final: 0.7963 (mm110)
REVERT: A   93 LEU cc_start: 0.9363 (mm) cc_final: 0.9086 (mm)
REVERT: A  124 MET cc_start: 0.8401 (tpp) cc_final: 0.7755 (tpp)
REVERT: A  246 ASP cc_start: 0.8782 (m-30) cc_final: 0.7814 (t0)
REVERT: A  372 CYS cc_start: 0.9023 (m) cc_final: 0.8685 (m)
REVERT: A  520 MET cc_start: 0.8711 (mmm) cc_final: 0.8115 (mmm)
REVERT: A  534 ASP cc_start: 0.8398 (t70) cc_final: 0.8065 (t70)
REVERT: A  614 LYS cc_start: 0.8161 (tttt) cc_final: 0.7628 (mttt)
REVERT: B    4 GLU cc_start: 0.6969 (pm20) cc_final: 0.6620 (tm-30)
REVERT: B   81 HIS cc_start: 0.8835 (m-70) cc_final: 0.8134 (m-70)
REVERT: B   95 PHE cc_start: 0.7715 (t80) cc_final: 0.7387 (t80)
REVERT: B  142 MET cc_start: 0.6528 (tpp) cc_final: 0.6160 (tpp)
REVERT: B  168 CYS cc_start: 0.9189 (m) cc_final: 0.8912 (m)
REVERT: B  204 PHE cc_start: 0.8020 (t80) cc_final: 0.7691 (t80)
REVERT: B  289 MET cc_start: 0.5761 (ttt) cc_final: 0.5279 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 318
  average time/residue: 0.1778
  time to fit residues: 82.7050
Evaluate side-chains
  256 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 35 optimal weight:    0.2980
   chunk 87 optimal weight:    8.9990
   chunk 110 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.157895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.128273 restraints weight = 21757.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127966 restraints weight = 14791.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128825 restraints weight = 12035.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9804  Z= 0.224
  Angle     :  0.644  10.318  13287  Z= 0.327
  Chirality :  0.041   0.175   1478
  Planarity :  0.004   0.062   1642
  Dihedral  :  4.857  24.347   1277
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.38 (0.25), residues: 1140
  helix:  1.04 (0.18), residues: 843
  sheet:  None (None), residues: 0
  loop : -2.02 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  96 
 HIS   0.010   0.001   HIS B  79 
 PHE   0.019   0.002   PHE D 534 
 TYR   0.019   0.001   TYR B 117 
 ARG   0.011   0.000   ARG A 579 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7190 (pttp)
REVERT: C   61 PHE cc_start: 0.7775 (m-80) cc_final: 0.7488 (m-80)
REVERT: C   71 MET cc_start: 0.8176 (tpt) cc_final: 0.7748 (tpt)
REVERT: C   75 PHE cc_start: 0.7778 (m-80) cc_final: 0.7299 (m-80)
REVERT: C   99 PHE cc_start: 0.5988 (m-80) cc_final: 0.5628 (m-80)
REVERT: C  120 VAL cc_start: 0.8386 (t) cc_final: 0.7213 (t)
REVERT: C  121 LEU cc_start: 0.9538 (mt) cc_final: 0.9238 (mt)
REVERT: C  137 GLN cc_start: 0.7643 (mt0) cc_final: 0.7335 (mt0)
REVERT: A   49 MET cc_start: 0.8155 (mmm) cc_final: 0.7526 (mmt)
REVERT: A   93 LEU cc_start: 0.9278 (mm) cc_final: 0.9060 (mm)
REVERT: A  246 ASP cc_start: 0.8792 (m-30) cc_final: 0.7591 (t0)
REVERT: A  372 CYS cc_start: 0.9070 (m) cc_final: 0.8730 (m)
REVERT: A  379 MET cc_start: 0.8316 (mtm) cc_final: 0.8102 (mtm)
REVERT: A  438 MET cc_start: 0.8250 (mmt) cc_final: 0.7901 (mmm)
REVERT: A  473 MET cc_start: 0.8889 (mmm) cc_final: 0.8680 (mmt)
REVERT: A  520 MET cc_start: 0.8831 (mmm) cc_final: 0.8581 (mmm)
REVERT: A  534 ASP cc_start: 0.8395 (t70) cc_final: 0.8039 (t70)
REVERT: A  614 LYS cc_start: 0.8052 (tttt) cc_final: 0.7624 (mttp)
REVERT: A  652 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8125 (tttt)
REVERT: B    4 GLU cc_start: 0.7067 (pm20) cc_final: 0.6743 (tm-30)
REVERT: B   36 LEU cc_start: 0.8773 (tp) cc_final: 0.8175 (mm)
REVERT: B   81 HIS cc_start: 0.8905 (m-70) cc_final: 0.8127 (m-70)
REVERT: B   95 PHE cc_start: 0.7612 (t80) cc_final: 0.7377 (t80)
REVERT: B  142 MET cc_start: 0.6551 (tpp) cc_final: 0.6170 (tpp)
REVERT: B  204 PHE cc_start: 0.8126 (t80) cc_final: 0.7746 (t80)
REVERT: B  289 MET cc_start: 0.5695 (ttt) cc_final: 0.5252 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.1843
  time to fit residues: 80.9913
Evaluate side-chains
  252 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 108 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 109 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    3.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.155145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.125161 restraints weight = 21941.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.124872 restraints weight = 14142.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125709 restraints weight = 12458.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9804  Z= 0.306
  Angle     :  0.682  10.524  13287  Z= 0.351
  Chirality :  0.043   0.181   1478
  Planarity :  0.004   0.049   1642
  Dihedral  :  4.940  25.923   1277
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.24 (0.25), residues: 1140
  helix:  0.91 (0.18), residues: 844
  sheet:  None (None), residues: 0
  loop : -1.99 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 122 
 PHE   0.019   0.002   PHE A 201 
 TYR   0.019   0.002   TYR C 165 
 ARG   0.003   0.000   ARG C  91 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7137 (pttp)
REVERT: C   71 MET cc_start: 0.8175 (tpt) cc_final: 0.7681 (tpt)
REVERT: C   75 PHE cc_start: 0.7831 (m-80) cc_final: 0.7338 (m-80)
REVERT: C   99 PHE cc_start: 0.6029 (m-80) cc_final: 0.5625 (m-80)
REVERT: C  120 VAL cc_start: 0.8540 (t) cc_final: 0.7373 (t)
REVERT: C  121 LEU cc_start: 0.9525 (mt) cc_final: 0.9289 (mt)
REVERT: C  137 GLN cc_start: 0.7742 (mt0) cc_final: 0.7420 (mt0)
REVERT: C  177 MET cc_start: 0.8280 (tpp) cc_final: 0.7761 (mmm)
REVERT: A   93 LEU cc_start: 0.9269 (mm) cc_final: 0.9068 (mm)
REVERT: A  372 CYS cc_start: 0.9091 (m) cc_final: 0.8732 (m)
REVERT: A  379 MET cc_start: 0.8432 (mtm) cc_final: 0.8166 (mtm)
REVERT: A  534 ASP cc_start: 0.8404 (t70) cc_final: 0.8070 (t70)
REVERT: A  614 LYS cc_start: 0.8109 (tttt) cc_final: 0.7787 (mttt)
REVERT: B    4 GLU cc_start: 0.7091 (pm20) cc_final: 0.6731 (tm-30)
REVERT: B   36 LEU cc_start: 0.8871 (tp) cc_final: 0.8219 (mm)
REVERT: B   51 LEU cc_start: 0.7821 (mt) cc_final: 0.7542 (tp)
REVERT: B   81 HIS cc_start: 0.8886 (m-70) cc_final: 0.8103 (m-70)
REVERT: B  142 MET cc_start: 0.6592 (tpp) cc_final: 0.6255 (tpp)
REVERT: B  204 PHE cc_start: 0.8128 (t80) cc_final: 0.7751 (t80)
REVERT: B  289 MET cc_start: 0.5605 (ttt) cc_final: 0.5272 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 301
  average time/residue: 0.1975
  time to fit residues: 86.9739
Evaluate side-chains
  251 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 70 optimal weight:    0.3980
   chunk 113 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 125 ASN
A 113 HIS
A 123 ASN
** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.159601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129018 restraints weight = 22001.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.129553 restraints weight = 14611.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.131426 restraints weight = 10628.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9804  Z= 0.174
  Angle     :  0.650  11.389  13287  Z= 0.327
  Chirality :  0.041   0.165   1478
  Planarity :  0.004   0.050   1642
  Dihedral  :  4.818  25.549   1277
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.37 (0.25), residues: 1140
  helix:  1.10 (0.18), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.27 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 122 
 PHE   0.023   0.001   PHE D 534 
 TYR   0.019   0.001   TYR A 425 
 ARG   0.007   0.000   ARG A 321 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 1.310 
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: D  770 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7089 (pttp)
REVERT: C   71 MET cc_start: 0.8232 (tpt) cc_final: 0.7744 (tpt)
REVERT: C   75 PHE cc_start: 0.7777 (m-80) cc_final: 0.7235 (m-80)
REVERT: C   99 PHE cc_start: 0.5869 (m-80) cc_final: 0.5503 (m-80)
REVERT: C  120 VAL cc_start: 0.8377 (t) cc_final: 0.7442 (t)
REVERT: C  121 LEU cc_start: 0.9535 (mt) cc_final: 0.9213 (mt)
REVERT: C  137 GLN cc_start: 0.7742 (mt0) cc_final: 0.7449 (mt0)
REVERT: A   49 MET cc_start: 0.7631 (mmt) cc_final: 0.7403 (mmt)
REVERT: A   93 LEU cc_start: 0.9261 (mm) cc_final: 0.8999 (mm)
REVERT: A  232 ILE cc_start: 0.8130 (mm) cc_final: 0.7866 (mm)
REVERT: A  372 CYS cc_start: 0.9058 (m) cc_final: 0.8695 (m)
REVERT: A  379 MET cc_start: 0.8371 (mtm) cc_final: 0.8120 (mtm)
REVERT: A  425 TYR cc_start: 0.7504 (m-10) cc_final: 0.7204 (m-10)
REVERT: A  434 ILE cc_start: 0.9363 (pt) cc_final: 0.9030 (pt)
REVERT: A  453 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8677 (mm-40)
REVERT: A  534 ASP cc_start: 0.8370 (t70) cc_final: 0.7897 (t0)
REVERT: A  614 LYS cc_start: 0.7895 (tttt) cc_final: 0.7574 (mttt)
REVERT: B    4 GLU cc_start: 0.7021 (pm20) cc_final: 0.6752 (tm-30)
REVERT: B   36 LEU cc_start: 0.8730 (tp) cc_final: 0.8225 (mm)
REVERT: B   81 HIS cc_start: 0.8900 (m-70) cc_final: 0.8022 (m-70)
REVERT: B   85 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.6803 (tpt170)
REVERT: B  142 MET cc_start: 0.6570 (tpp) cc_final: 0.6252 (tpp)
REVERT: B  168 CYS cc_start: 0.9182 (m) cc_final: 0.8858 (m)
REVERT: B  204 PHE cc_start: 0.8110 (t80) cc_final: 0.7732 (t80)
REVERT: B  289 MET cc_start: 0.6085 (ttt) cc_final: 0.5601 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 320
  average time/residue: 0.2513
  time to fit residues: 118.0708
Evaluate side-chains
  258 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 108 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0980
   overall best weight:    3.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
A 564 GLN
B  79 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.153865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.123486 restraints weight = 21600.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122962 restraints weight = 15922.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.124061 restraints weight = 15552.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9804  Z= 0.321
  Angle     :  0.728  10.933  13287  Z= 0.376
  Chirality :  0.045   0.195   1478
  Planarity :  0.005   0.049   1642
  Dihedral  :  4.989  26.153   1277
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.16 (0.25), residues: 1140
  helix:  0.91 (0.17), residues: 839
  sheet:  None (None), residues: 0
  loop : -2.14 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP C 169 
 HIS   0.007   0.002   HIS B 122 
 PHE   0.022   0.002   PHE D 534 
 TYR   0.024   0.002   TYR C 165 
 ARG   0.006   0.001   ARG C  91 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7096 (pttp)
REVERT: C   71 MET cc_start: 0.8244 (tpt) cc_final: 0.7560 (tpt)
REVERT: C   75 PHE cc_start: 0.7843 (m-80) cc_final: 0.7307 (m-80)
REVERT: C   99 PHE cc_start: 0.5955 (m-80) cc_final: 0.5558 (m-80)
REVERT: C  120 VAL cc_start: 0.8474 (t) cc_final: 0.7547 (t)
REVERT: C  121 LEU cc_start: 0.9541 (mt) cc_final: 0.9324 (mt)
REVERT: C  137 GLN cc_start: 0.7653 (mt0) cc_final: 0.7318 (mt0)
REVERT: C  157 MET cc_start: 0.7228 (ppp) cc_final: 0.6778 (ppp)
REVERT: C  191 LYS cc_start: 0.7816 (tmtt) cc_final: 0.7341 (tmtt)
REVERT: A  372 CYS cc_start: 0.9019 (m) cc_final: 0.8693 (m)
REVERT: A  374 GLN cc_start: 0.8543 (mt0) cc_final: 0.8028 (mm-40)
REVERT: A  379 MET cc_start: 0.8506 (mtm) cc_final: 0.8273 (mtm)
REVERT: A  438 MET cc_start: 0.8490 (mmp) cc_final: 0.8130 (mmm)
REVERT: A  499 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7524 (tptm)
REVERT: A  534 ASP cc_start: 0.8459 (t70) cc_final: 0.8040 (t0)
REVERT: A  614 LYS cc_start: 0.8203 (tttt) cc_final: 0.7853 (mttp)
REVERT: B   36 LEU cc_start: 0.8711 (tp) cc_final: 0.7954 (mm)
REVERT: B   81 HIS cc_start: 0.8872 (m-70) cc_final: 0.8016 (m-70)
REVERT: B  168 CYS cc_start: 0.9005 (m) cc_final: 0.8775 (m)
REVERT: B  204 PHE cc_start: 0.8209 (t80) cc_final: 0.7866 (t80)
REVERT: B  278 THR cc_start: 0.8712 (p) cc_final: 0.7826 (p)
REVERT: B  279 ARG cc_start: 0.8685 (mmp80) cc_final: 0.7826 (mmp-170)
REVERT: B  289 MET cc_start: 0.6155 (ttt) cc_final: 0.5672 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.2029
  time to fit residues: 87.7618
Evaluate side-chains
  248 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 97 optimal weight:    0.1980
   chunk 74 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
** B  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.160477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.130509 restraints weight = 21478.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.128936 restraints weight = 13963.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130219 restraints weight = 12289.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9804  Z= 0.173
  Angle     :  0.680  11.299  13287  Z= 0.339
  Chirality :  0.042   0.196   1478
  Planarity :  0.004   0.051   1642
  Dihedral  :  4.803  24.069   1277
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.34 (0.25), residues: 1140
  helix:  1.10 (0.17), residues: 840
  sheet:  None (None), residues: 0
  loop : -2.31 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  27 
 HIS   0.007   0.001   HIS B  79 
 PHE   0.017   0.001   PHE B  95 
 TYR   0.018   0.001   TYR A 425 
 ARG   0.003   0.000   ARG C  55 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7895 (mmtt) cc_final: 0.6966 (pttp)
REVERT: C   71 MET cc_start: 0.8242 (tpt) cc_final: 0.7701 (tpt)
REVERT: C   75 PHE cc_start: 0.7613 (m-80) cc_final: 0.7027 (m-80)
REVERT: C   99 PHE cc_start: 0.5976 (m-80) cc_final: 0.5575 (m-80)
REVERT: C  120 VAL cc_start: 0.8448 (t) cc_final: 0.7757 (t)
REVERT: C  121 LEU cc_start: 0.9594 (mt) cc_final: 0.9284 (mt)
REVERT: A  372 CYS cc_start: 0.9043 (m) cc_final: 0.8682 (m)
REVERT: A  374 GLN cc_start: 0.8504 (mt0) cc_final: 0.8009 (mm-40)
REVERT: A  379 MET cc_start: 0.8440 (mtm) cc_final: 0.8146 (mtm)
REVERT: A  534 ASP cc_start: 0.8432 (t70) cc_final: 0.8027 (t0)
REVERT: A  614 LYS cc_start: 0.7965 (tttt) cc_final: 0.7663 (mttp)
REVERT: A  652 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8215 (tttt)
REVERT: B    1 MET cc_start: 0.0762 (mmt) cc_final: 0.0181 (mtt)
REVERT: B    4 GLU cc_start: 0.7169 (pm20) cc_final: 0.6810 (tm-30)
REVERT: B   19 LEU cc_start: 0.8867 (mm) cc_final: 0.8542 (mm)
REVERT: B   36 LEU cc_start: 0.8732 (tp) cc_final: 0.8188 (mm)
REVERT: B   37 GLN cc_start: 0.8906 (tt0) cc_final: 0.8434 (tt0)
REVERT: B   81 HIS cc_start: 0.8886 (m-70) cc_final: 0.8018 (m-70)
REVERT: B  168 CYS cc_start: 0.9049 (m) cc_final: 0.8669 (m)
REVERT: B  204 PHE cc_start: 0.8179 (t80) cc_final: 0.7876 (t80)
REVERT: B  289 MET cc_start: 0.6377 (ttt) cc_final: 0.5720 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 318
  average time/residue: 0.1838
  time to fit residues: 84.0584
Evaluate side-chains
  251 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 4 optimal weight:    0.3980
   chunk 66 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
** B  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.159806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128787 restraints weight = 21467.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.129943 restraints weight = 13656.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.130968 restraints weight = 11572.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9804  Z= 0.197
  Angle     :  0.672  11.209  13287  Z= 0.337
  Chirality :  0.042   0.191   1478
  Planarity :  0.004   0.053   1642
  Dihedral  :  4.753  24.276   1277
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  0.34 (0.25), residues: 1140
  helix:  1.08 (0.17), residues: 843
  sheet:  None (None), residues: 0
  loop : -2.28 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 122 
 PHE   0.038   0.002   PHE C 176 
 TYR   0.030   0.002   TYR B 117 
 ARG   0.002   0.000   ARG C  91 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3187.76 seconds
wall clock time: 57 minutes 49.71 seconds (3469.71 seconds total)