Starting phenix.real_space_refine
on Wed Mar  4 00:03:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vk0_21222/03_2026/6vk0_21222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vk0_21222/03_2026/6vk0_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_2026/6vk0_21222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2026/6vk0_21222.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2026/6vk0_21222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vk0_21222/03_2026/6vk0_21222.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.91, per 1000 atoms: 0.20
  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: 0.63
  Conformation dependent library (CDL) restraints added in 303.4 milliseconds
  

  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: 0.22
  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: 1.15

  Time building geometry restraints manager: 0.86 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:             0.260
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.070
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.850
-------------------------------------------------------------------------------
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= 0.322
  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 : 17.51
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.009   0.001   ARG A 265 
 TYR   0.029   0.002   TYR B  18 
 PHE   0.033   0.002   PHE B  88 
 TRP   0.018   0.002   TRP A 684 
 HIS   0.011   0.002   HIS B 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 9804)
  covalent geometry    : angle       0.84432 (13287)
  hydrogen bonds       : bond        0.15407 (  616)
  hydrogen bonds       : angle       6.83439 ( 1842)

*********************** 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  : 0.256 
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: 0.6223 (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: 0.8182 (mt0) cc_final: 0.7698 (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: 0.6752 (mmm)
REVERT: A  439 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7737 (mtpt)
REVERT: A  461 PHE cc_start: 0.8369 (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: 0.8841 (mtm)
  outliers start: 2
  outliers final: 1
  residues processed: 322
  average time/residue: 0.0985
  time to fit residues: 43.4922
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  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.2980
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:   20.0000
   overall best weight:    3.2586

-------------------------------------------------------------------------------
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 117 GLN
A 135 ASN
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: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.152676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.121564 restraints weight = 21480.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120541 restraints weight = 14731.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.121197 restraints weight = 12486.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.121728 restraints weight = 10895.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.122261 restraints weight = 9791.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9804  Z= 0.213
  Angle     :  0.709  11.836  13287  Z= 0.375
  Chirality :  0.044   0.163   1478
  Planarity :  0.005   0.088   1642
  Dihedral  :  5.616  28.085   1277
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  6.12 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.23), residues: 1140
  helix: -0.36 (0.17), residues: 829
  sheet:  None (None), residues: 0
  loop : -2.21 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 589 
 TYR   0.019   0.002   TYR C  42 
 PHE   0.035   0.002   PHE D 534 
 TRP   0.033   0.002   TRP C  19 
 HIS   0.012   0.002   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 9804)
  covalent geometry    : angle       0.70898 (13287)
  hydrogen bonds       : bond        0.05926 (  616)
  hydrogen bonds       : angle       5.20882 ( 1842)

*********************** 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
  324 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 322
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7481 (mmtt) cc_final: 0.6336 (pttp)
REVERT: C   39 LYS cc_start: 0.5768 (mttt) cc_final: 0.5224 (mmtt)
REVERT: C   52 GLN cc_start: 0.5702 (tp-100) cc_final: 0.5252 (tp40)
REVERT: C   75 PHE cc_start: 0.7814 (m-80) cc_final: 0.7539 (m-80)
REVERT: C   91 ARG cc_start: 0.7300 (mpt180) cc_final: 0.6788 (mtt180)
REVERT: C   99 PHE cc_start: 0.6458 (m-80) cc_final: 0.5785 (m-80)
REVERT: C  112 GLU cc_start: 0.6777 (pm20) cc_final: 0.5198 (tm-30)
REVERT: C  130 GLU cc_start: 0.7917 (tp30) cc_final: 0.7631 (tp30)
REVERT: C  137 GLN cc_start: 0.8119 (mt0) cc_final: 0.7690 (mt0)
REVERT: C  166 LYS cc_start: 0.8341 (tppt) cc_final: 0.7897 (tptp)
REVERT: A   79 GLN cc_start: 0.8003 (mm110) cc_final: 0.7756 (mm110)
REVERT: A   90 TYR cc_start: 0.7728 (t80) cc_final: 0.7423 (t80)
REVERT: A   93 LEU cc_start: 0.9487 (mm) cc_final: 0.9220 (mm)
REVERT: A  246 ASP cc_start: 0.8861 (m-30) cc_final: 0.8588 (m-30)
REVERT: A  372 CYS cc_start: 0.9062 (m) cc_final: 0.8654 (m)
REVERT: A  438 MET cc_start: 0.7812 (mmm) cc_final: 0.7261 (mmt)
REVERT: A  461 PHE cc_start: 0.8148 (m-80) cc_final: 0.7844 (m-10)
REVERT: A  514 ASP cc_start: 0.8401 (m-30) cc_final: 0.8064 (m-30)
REVERT: A  520 MET cc_start: 0.8965 (mmm) cc_final: 0.8580 (mmm)
REVERT: A  537 GLU cc_start: 0.7415 (tp30) cc_final: 0.7092 (tp30)
REVERT: A  571 ASP cc_start: 0.8669 (t0) cc_final: 0.8441 (t0)
REVERT: A  614 LYS cc_start: 0.8403 (tttt) cc_final: 0.7980 (mttt)
REVERT: A  639 GLU cc_start: 0.8925 (pp20) cc_final: 0.8097 (pp20)
REVERT: A  666 TYR cc_start: 0.7998 (t80) cc_final: 0.7783 (t80)
REVERT: A  679 LYS cc_start: 0.8352 (mttt) cc_final: 0.8099 (mtpp)
REVERT: B    4 GLU cc_start: 0.7161 (pm20) cc_final: 0.6574 (tm-30)
REVERT: B   36 LEU cc_start: 0.8834 (tp) cc_final: 0.8148 (mm)
REVERT: B   80 GLU cc_start: 0.8897 (mp0) cc_final: 0.8624 (mp0)
REVERT: B   81 HIS cc_start: 0.8911 (m-70) cc_final: 0.8130 (m-70)
REVERT: B   95 PHE cc_start: 0.7366 (t80) cc_final: 0.6985 (t80)
REVERT: B  142 MET cc_start: 0.6988 (tpp) cc_final: 0.6691 (tpp)
REVERT: B  195 MET cc_start: 0.9023 (mtp) cc_final: 0.8702 (mtm)
REVERT: B  289 MET cc_start: 0.6285 (ttt) cc_final: 0.5311 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 323
  average time/residue: 0.0827
  time to fit residues: 38.4300
Evaluate side-chains
  263 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 262
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 83 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 51 optimal weight:    0.4980
   chunk 43 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
A 123 ASN
B 189 GLN
B 312 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.155630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125092 restraints weight = 21582.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125756 restraints weight = 14075.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126783 restraints weight = 11855.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.127283 restraints weight = 8905.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.127371 restraints weight = 8749.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9804  Z= 0.169
  Angle     :  0.655  10.888  13287  Z= 0.343
  Chirality :  0.042   0.207   1478
  Planarity :  0.004   0.058   1642
  Dihedral  :  5.374  28.076   1277
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.25), residues: 1140
  helix:  0.37 (0.18), residues: 838
  sheet:  None (None), residues: 0
  loop : -2.02 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  55 
 TYR   0.016   0.002   TYR A 240 
 PHE   0.026   0.002   PHE D 544 
 TRP   0.022   0.002   TRP A  27 
 HIS   0.005   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9804)
  covalent geometry    : angle       0.65503 (13287)
  hydrogen bonds       : bond        0.05253 (  616)
  hydrogen bonds       : angle       4.78428 ( 1842)

*********************** 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
  323 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 321
  time to evaluate  : 0.274 
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: 0.7836 (mmtt) cc_final: 0.6883 (pttp)
REVERT: C   39 LYS cc_start: 0.5918 (mttt) cc_final: 0.5415 (mmtt)
REVERT: C   71 MET cc_start: 0.8188 (mmm) cc_final: 0.7881 (tpt)
REVERT: C   75 PHE cc_start: 0.7768 (m-80) cc_final: 0.6818 (m-80)
REVERT: C   91 ARG cc_start: 0.7142 (mpt180) cc_final: 0.6577 (mtt180)
REVERT: C   99 PHE cc_start: 0.6325 (m-80) cc_final: 0.5719 (m-80)
REVERT: C  109 THR cc_start: 0.7841 (t) cc_final: 0.7193 (t)
REVERT: C  112 GLU cc_start: 0.7164 (pm20) cc_final: 0.5270 (tm-30)
REVERT: C  121 LEU cc_start: 0.9408 (mt) cc_final: 0.9097 (mt)
REVERT: C  130 GLU cc_start: 0.7935 (tp30) cc_final: 0.7649 (tp30)
REVERT: C  137 GLN cc_start: 0.7868 (mt0) cc_final: 0.7468 (mt0)
REVERT: A   74 TYR cc_start: 0.8155 (t80) cc_final: 0.7910 (t80)
REVERT: A   79 GLN cc_start: 0.7961 (mm110) cc_final: 0.7682 (mm110)
REVERT: A   90 TYR cc_start: 0.7763 (t80) cc_final: 0.7305 (t80)
REVERT: A   93 LEU cc_start: 0.9394 (mm) cc_final: 0.9100 (mm)
REVERT: A  246 ASP cc_start: 0.9026 (m-30) cc_final: 0.8576 (m-30)
REVERT: A  372 CYS cc_start: 0.9037 (m) cc_final: 0.8626 (m)
REVERT: A  520 MET cc_start: 0.8786 (mmm) cc_final: 0.8484 (mmm)
REVERT: A  571 ASP cc_start: 0.8716 (t0) cc_final: 0.8514 (t0)
REVERT: A  614 LYS cc_start: 0.8340 (tttt) cc_final: 0.7989 (mttt)
REVERT: A  639 GLU cc_start: 0.8880 (pp20) cc_final: 0.8395 (pp20)
REVERT: B    1 MET cc_start: 0.3128 (mmt) cc_final: 0.2717 (mmt)
REVERT: B    4 GLU cc_start: 0.7133 (pm20) cc_final: 0.6553 (tm-30)
REVERT: B   36 LEU cc_start: 0.8798 (tp) cc_final: 0.8244 (mm)
REVERT: B   81 HIS cc_start: 0.8827 (m-70) cc_final: 0.8037 (m90)
REVERT: B   95 PHE cc_start: 0.7316 (t80) cc_final: 0.6961 (t80)
REVERT: B  142 MET cc_start: 0.6688 (tpp) cc_final: 0.6378 (tpp)
REVERT: B  192 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8525 (mm-30)
REVERT: B  195 MET cc_start: 0.8975 (mtp) cc_final: 0.8720 (mtm)
REVERT: B  204 PHE cc_start: 0.8096 (t80) cc_final: 0.7662 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 321
  average time/residue: 0.0781
  time to fit residues: 37.0369
Evaluate side-chains
  268 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0070
   chunk 1 optimal weight:    7.9990
   chunk 96 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.4004

-------------------------------------------------------------------------------
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
A 113 HIS
A 564 GLN
A 611 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.154948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.125145 restraints weight = 21981.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.124186 restraints weight = 14854.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125492 restraints weight = 14010.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.126289 restraints weight = 10316.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.126700 restraints weight = 9448.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9804  Z= 0.165
  Angle     :  0.643  10.659  13287  Z= 0.334
  Chirality :  0.042   0.169   1478
  Planarity :  0.004   0.058   1642
  Dihedral  :  5.202  26.819   1277
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.25), residues: 1140
  helix:  0.69 (0.18), residues: 835
  sheet:  None (None), residues: 0
  loop : -1.88 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 141 
 TYR   0.014   0.001   TYR A 666 
 PHE   0.020   0.002   PHE D 544 
 TRP   0.023   0.002   TRP A  27 
 HIS   0.005   0.001   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9804)
  covalent geometry    : angle       0.64317 (13287)
  hydrogen bonds       : bond        0.04991 (  616)
  hydrogen bonds       : angle       4.61141 ( 1842)

*********************** 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
  319 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.378 
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: 0.7993 (mmtt) cc_final: 0.7186 (pttp)
REVERT: C   39 LYS cc_start: 0.5935 (mttt) cc_final: 0.5428 (mmtt)
REVERT: C   71 MET cc_start: 0.8056 (mmm) cc_final: 0.7638 (tpt)
REVERT: C   75 PHE cc_start: 0.7847 (m-80) cc_final: 0.6940 (m-80)
REVERT: C   99 PHE cc_start: 0.6197 (m-80) cc_final: 0.5655 (m-80)
REVERT: C  120 VAL cc_start: 0.8502 (t) cc_final: 0.7222 (t)
REVERT: C  121 LEU cc_start: 0.9414 (mt) cc_final: 0.9170 (mt)
REVERT: C  137 GLN cc_start: 0.7847 (mt0) cc_final: 0.7623 (tt0)
REVERT: A   79 GLN cc_start: 0.8016 (mm110) cc_final: 0.7705 (mm110)
REVERT: A   90 TYR cc_start: 0.7709 (t80) cc_final: 0.7209 (t80)
REVERT: A   93 LEU cc_start: 0.9452 (mm) cc_final: 0.9141 (mm)
REVERT: A  372 CYS cc_start: 0.9045 (m) cc_final: 0.8668 (m)
REVERT: A  438 MET cc_start: 0.8075 (mmt) cc_final: 0.7649 (mmm)
REVERT: A  520 MET cc_start: 0.8713 (mmm) cc_final: 0.8425 (mmm)
REVERT: A  534 ASP cc_start: 0.8393 (t70) cc_final: 0.8073 (t70)
REVERT: A  571 ASP cc_start: 0.8600 (t0) cc_final: 0.8258 (t0)
REVERT: A  614 LYS cc_start: 0.8353 (tttt) cc_final: 0.7910 (mttp)
REVERT: A  639 GLU cc_start: 0.8893 (pp20) cc_final: 0.8336 (pp20)
REVERT: A  652 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8241 (tttt)
REVERT: A  679 LYS cc_start: 0.8320 (mttt) cc_final: 0.8101 (mtpp)
REVERT: B    4 GLU cc_start: 0.7186 (pm20) cc_final: 0.6719 (tm-30)
REVERT: B   32 SER cc_start: 0.8518 (t) cc_final: 0.7956 (t)
REVERT: B   36 LEU cc_start: 0.8785 (tp) cc_final: 0.8169 (mm)
REVERT: B   37 GLN cc_start: 0.8861 (tt0) cc_final: 0.8263 (tt0)
REVERT: B   81 HIS cc_start: 0.8839 (m-70) cc_final: 0.8035 (m90)
REVERT: B  142 MET cc_start: 0.6650 (tpp) cc_final: 0.6287 (tpp)
REVERT: B  168 CYS cc_start: 0.9197 (m) cc_final: 0.8945 (m)
REVERT: B  195 MET cc_start: 0.8985 (mtp) cc_final: 0.8742 (mtm)
REVERT: B  204 PHE cc_start: 0.8153 (t80) cc_final: 0.7772 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 319
  average time/residue: 0.0738
  time to fit residues: 35.0011
Evaluate side-chains
  272 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.159259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.129170 restraints weight = 21705.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128953 restraints weight = 13722.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129643 restraints weight = 11476.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130217 restraints weight = 10186.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.130738 restraints weight = 9055.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3651

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= 0.129
  Angle     :  0.630  10.825  13287  Z= 0.324
  Chirality :  0.041   0.208   1478
  Planarity :  0.004   0.050   1642
  Dihedral  :  5.006  25.279   1277
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.25), residues: 1140
  helix:  0.89 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -2.10 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 542 
 TYR   0.020   0.001   TYR B  18 
 PHE   0.020   0.001   PHE D 534 
 TRP   0.026   0.001   TRP A  27 
 HIS   0.005   0.001   HIS B 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9804)
  covalent geometry    : angle       0.62963 (13287)
  hydrogen bonds       : bond        0.04597 (  616)
  hydrogen bonds       : angle       4.34201 ( 1842)

*********************** 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
  330 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 330
  time to evaluate  : 0.357 
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: 0.7898 (mmtt) cc_final: 0.7110 (pttp)
REVERT: C   71 MET cc_start: 0.8212 (mmm) cc_final: 0.7800 (tpt)
REVERT: C   75 PHE cc_start: 0.7858 (m-80) cc_final: 0.6995 (m-80)
REVERT: C   99 PHE cc_start: 0.6197 (m-80) cc_final: 0.5771 (m-80)
REVERT: C  109 THR cc_start: 0.7304 (t) cc_final: 0.6970 (t)
REVERT: C  112 GLU cc_start: 0.7787 (pm20) cc_final: 0.6729 (tm-30)
REVERT: C  120 VAL cc_start: 0.8322 (t) cc_final: 0.7150 (t)
REVERT: C  121 LEU cc_start: 0.9518 (mt) cc_final: 0.9291 (mt)
REVERT: C  122 LEU cc_start: 0.9384 (mm) cc_final: 0.9182 (mm)
REVERT: C  125 ASN cc_start: 0.8766 (m-40) cc_final: 0.8556 (m110)
REVERT: C  137 GLN cc_start: 0.7677 (mt0) cc_final: 0.7330 (mt0)
REVERT: C  187 ASP cc_start: 0.7418 (m-30) cc_final: 0.7078 (m-30)
REVERT: A   74 TYR cc_start: 0.7696 (t80) cc_final: 0.7097 (t80)
REVERT: A   93 LEU cc_start: 0.9462 (mm) cc_final: 0.9095 (mm)
REVERT: A  132 GLU cc_start: 0.7725 (tp30) cc_final: 0.6650 (tp30)
REVERT: A  180 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.8059 (tpp-160)
REVERT: A  246 ASP cc_start: 0.8883 (m-30) cc_final: 0.8378 (m-30)
REVERT: A  372 CYS cc_start: 0.8999 (m) cc_final: 0.8637 (m)
REVERT: A  434 ILE cc_start: 0.9391 (mp) cc_final: 0.9064 (pt)
REVERT: A  520 MET cc_start: 0.8695 (mmm) cc_final: 0.8125 (mmm)
REVERT: A  534 ASP cc_start: 0.8329 (t70) cc_final: 0.8013 (t70)
REVERT: A  614 LYS cc_start: 0.8022 (tttt) cc_final: 0.7591 (mttp)
REVERT: A  639 GLU cc_start: 0.8773 (pp20) cc_final: 0.8411 (pp20)
REVERT: B    4 GLU cc_start: 0.7022 (pm20) cc_final: 0.6628 (tm-30)
REVERT: B   81 HIS cc_start: 0.8916 (m-70) cc_final: 0.8007 (m90)
REVERT: B   85 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.6658 (tpt170)
REVERT: B   95 PHE cc_start: 0.7708 (t80) cc_final: 0.7495 (t80)
REVERT: B  142 MET cc_start: 0.6629 (tpp) cc_final: 0.6251 (tpp)
REVERT: B  168 CYS cc_start: 0.9225 (m) cc_final: 0.8850 (m)
REVERT: B  192 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8426 (mm-30)
REVERT: B  204 PHE cc_start: 0.8153 (t80) cc_final: 0.7774 (t80)
REVERT: B  312 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7410 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 330
  average time/residue: 0.0779
  time to fit residues: 37.4799
Evaluate side-chains
  272 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.153882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.123393 restraints weight = 21853.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122680 restraints weight = 15308.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.123273 restraints weight = 12826.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.123550 restraints weight = 11694.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.125413 restraints weight = 10358.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9804  Z= 0.221
  Angle     :  0.712   9.844  13287  Z= 0.367
  Chirality :  0.044   0.205   1478
  Planarity :  0.005   0.052   1642
  Dihedral  :  5.156  26.617   1277
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.06 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1140
  helix:  0.78 (0.18), residues: 842
  sheet:  None (None), residues: 0
  loop : -2.03 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  91 
 TYR   0.020   0.002   TYR A 636 
 PHE   0.022   0.002   PHE D 534 
 TRP   0.040   0.002   TRP C 169 
 HIS   0.005   0.001   HIS A 638 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 9804)
  covalent geometry    : angle       0.71198 (13287)
  hydrogen bonds       : bond        0.05064 (  616)
  hydrogen bonds       : angle       4.61221 ( 1842)

*********************** 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
  301 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 300
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7181 (pttp)
REVERT: C   71 MET cc_start: 0.8222 (mmm) cc_final: 0.7714 (tpt)
REVERT: C   75 PHE cc_start: 0.7914 (m-80) cc_final: 0.7069 (m-80)
REVERT: C   99 PHE cc_start: 0.6228 (m-80) cc_final: 0.5798 (m-80)
REVERT: C  120 VAL cc_start: 0.8413 (t) cc_final: 0.7153 (t)
REVERT: C  121 LEU cc_start: 0.9561 (mt) cc_final: 0.9294 (mt)
REVERT: C  137 GLN cc_start: 0.7743 (mt0) cc_final: 0.7524 (tt0)
REVERT: C  166 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7213 (mmmt)
REVERT: C  177 MET cc_start: 0.8479 (tpp) cc_final: 0.7883 (mmm)
REVERT: C  187 ASP cc_start: 0.7741 (m-30) cc_final: 0.7382 (m-30)
REVERT: C  191 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7251 (tmtt)
REVERT: A   93 LEU cc_start: 0.9325 (mm) cc_final: 0.9058 (mm)
REVERT: A  246 ASP cc_start: 0.8989 (m-30) cc_final: 0.8539 (m-30)
REVERT: A  372 CYS cc_start: 0.9041 (m) cc_final: 0.8674 (m)
REVERT: A  434 ILE cc_start: 0.9417 (mp) cc_final: 0.8995 (mp)
REVERT: A  438 MET cc_start: 0.8196 (mmp) cc_final: 0.7887 (mmm)
REVERT: A  520 MET cc_start: 0.8704 (mmm) cc_final: 0.8379 (mmm)
REVERT: A  534 ASP cc_start: 0.8386 (t70) cc_final: 0.8061 (t70)
REVERT: A  614 LYS cc_start: 0.8105 (tttt) cc_final: 0.7786 (mttt)
REVERT: B    4 GLU cc_start: 0.7064 (pm20) cc_final: 0.6688 (tm-30)
REVERT: B   36 LEU cc_start: 0.8834 (tp) cc_final: 0.8119 (mm)
REVERT: B   51 LEU cc_start: 0.7953 (mt) cc_final: 0.7745 (tp)
REVERT: B   81 HIS cc_start: 0.8912 (m-70) cc_final: 0.8014 (m90)
REVERT: B   95 PHE cc_start: 0.7677 (t80) cc_final: 0.7448 (t80)
REVERT: B  142 MET cc_start: 0.6813 (tpp) cc_final: 0.6591 (tpp)
REVERT: B  168 CYS cc_start: 0.9083 (m) cc_final: 0.8768 (m)
REVERT: B  204 PHE cc_start: 0.8192 (t80) cc_final: 0.7835 (t80)
REVERT: B  312 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7646 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 301
  average time/residue: 0.0774
  time to fit residues: 34.5928
Evaluate side-chains
  255 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0770
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 80 optimal weight:    0.0470
   chunk 93 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.0040

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
** B 101 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 = 0.4023 r_free = 0.4023 target = 0.158887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.128945 restraints weight = 21673.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129390 restraints weight = 14003.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.130215 restraints weight = 10962.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.130960 restraints weight = 9384.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131059 restraints weight = 8614.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4108

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= 0.126
  Angle     :  0.638  11.231  13287  Z= 0.325
  Chirality :  0.041   0.167   1478
  Planarity :  0.004   0.047   1642
  Dihedral  :  4.956  25.163   1277
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.25), residues: 1140
  helix:  1.06 (0.18), residues: 843
  sheet:  None (None), residues: 0
  loop : -2.29 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  91 
 TYR   0.022   0.001   TYR A 636 
 PHE   0.020   0.001   PHE D 534 
 TRP   0.051   0.002   TRP C 169 
 HIS   0.006   0.001   HIS C 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9804)
  covalent geometry    : angle       0.63845 (13287)
  hydrogen bonds       : bond        0.04411 (  616)
  hydrogen bonds       : angle       4.28471 ( 1842)

*********************** 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
  316 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  770 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7111 (pttp)
REVERT: C   71 MET cc_start: 0.8081 (mmm) cc_final: 0.7680 (tpt)
REVERT: C   75 PHE cc_start: 0.7812 (m-80) cc_final: 0.7135 (m-80)
REVERT: C   99 PHE cc_start: 0.5914 (m-80) cc_final: 0.5551 (m-80)
REVERT: C  120 VAL cc_start: 0.8381 (t) cc_final: 0.7150 (t)
REVERT: C  121 LEU cc_start: 0.9528 (mt) cc_final: 0.9242 (mt)
REVERT: C  132 LYS cc_start: 0.8133 (tppt) cc_final: 0.7684 (tppt)
REVERT: C  137 GLN cc_start: 0.7733 (mt0) cc_final: 0.7462 (mt0)
REVERT: C  187 ASP cc_start: 0.7629 (m-30) cc_final: 0.7364 (m-30)
REVERT: A   74 TYR cc_start: 0.7639 (t80) cc_final: 0.7000 (t80)
REVERT: A   93 LEU cc_start: 0.9371 (mm) cc_final: 0.9077 (mm)
REVERT: A  138 THR cc_start: 0.8316 (m) cc_final: 0.8069 (t)
REVERT: A  372 CYS cc_start: 0.8992 (m) cc_final: 0.8619 (m)
REVERT: A  473 MET cc_start: 0.8836 (mmm) cc_final: 0.8625 (mmt)
REVERT: A  520 MET cc_start: 0.8699 (mmm) cc_final: 0.8165 (mmm)
REVERT: A  534 ASP cc_start: 0.8329 (t70) cc_final: 0.8007 (t70)
REVERT: A  614 LYS cc_start: 0.7963 (tttt) cc_final: 0.7688 (mttt)
REVERT: A  652 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8192 (tttt)
REVERT: B    4 GLU cc_start: 0.6950 (pm20) cc_final: 0.6613 (tm-30)
REVERT: B   36 LEU cc_start: 0.8610 (tp) cc_final: 0.8210 (mm)
REVERT: B   81 HIS cc_start: 0.8916 (m-70) cc_final: 0.8032 (m-70)
REVERT: B  142 MET cc_start: 0.6723 (tpp) cc_final: 0.6409 (tpp)
REVERT: B  168 CYS cc_start: 0.9004 (m) cc_final: 0.8626 (m)
REVERT: B  188 ILE cc_start: 0.9277 (tt) cc_final: 0.8935 (tt)
REVERT: B  204 PHE cc_start: 0.8092 (t80) cc_final: 0.7776 (t80)
REVERT: B  312 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7422 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 316
  average time/residue: 0.0753
  time to fit residues: 35.1395
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  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 109 optimal weight:    0.0010
   chunk 99 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 123 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.158007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.128446 restraints weight = 21778.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.127531 restraints weight = 16171.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128441 restraints weight = 14343.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129503 restraints weight = 10766.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.129602 restraints weight = 9537.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4299

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= 0.139
  Angle     :  0.648  11.224  13287  Z= 0.330
  Chirality :  0.042   0.195   1478
  Planarity :  0.004   0.045   1642
  Dihedral  :  4.862  26.482   1277
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.25), residues: 1140
  helix:  1.11 (0.18), residues: 837
  sheet:  None (None), residues: 0
  loop : -2.21 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  91 
 TYR   0.023   0.001   TYR C 165 
 PHE   0.020   0.002   PHE D 534 
 TRP   0.034   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9804)
  covalent geometry    : angle       0.64791 (13287)
  hydrogen bonds       : bond        0.04447 (  616)
  hydrogen bonds       : angle       4.31427 ( 1842)

*********************** 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
  308 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.459 
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: 0.7925 (mmtt) cc_final: 0.7022 (pttp)
REVERT: C   71 MET cc_start: 0.8090 (mmm) cc_final: 0.7650 (tpt)
REVERT: C   75 PHE cc_start: 0.7837 (m-80) cc_final: 0.7159 (m-80)
REVERT: C   99 PHE cc_start: 0.5929 (m-80) cc_final: 0.5572 (m-80)
REVERT: C  120 VAL cc_start: 0.8456 (t) cc_final: 0.7356 (t)
REVERT: C  121 LEU cc_start: 0.9589 (mt) cc_final: 0.9286 (mt)
REVERT: C  130 GLU cc_start: 0.7989 (tp30) cc_final: 0.7770 (tp30)
REVERT: C  137 GLN cc_start: 0.7734 (mt0) cc_final: 0.7452 (mt0)
REVERT: C  187 ASP cc_start: 0.7261 (m-30) cc_final: 0.6914 (m-30)
REVERT: A   74 TYR cc_start: 0.7638 (t80) cc_final: 0.7097 (t80)
REVERT: A   93 LEU cc_start: 0.9371 (mm) cc_final: 0.9090 (mm)
REVERT: A  138 THR cc_start: 0.8344 (m) cc_final: 0.8085 (t)
REVERT: A  246 ASP cc_start: 0.8863 (m-30) cc_final: 0.8333 (m-30)
REVERT: A  372 CYS cc_start: 0.8994 (m) cc_final: 0.8671 (m)
REVERT: A  520 MET cc_start: 0.8725 (mmm) cc_final: 0.8144 (mmm)
REVERT: A  534 ASP cc_start: 0.8364 (t70) cc_final: 0.7920 (t0)
REVERT: A  571 ASP cc_start: 0.8543 (t0) cc_final: 0.8328 (t0)
REVERT: A  614 LYS cc_start: 0.8071 (tttt) cc_final: 0.7675 (mttt)
REVERT: B   36 LEU cc_start: 0.8797 (tp) cc_final: 0.8300 (mm)
REVERT: B   81 HIS cc_start: 0.8989 (m-70) cc_final: 0.8060 (m-70)
REVERT: B  142 MET cc_start: 0.6500 (tpp) cc_final: 0.6233 (tpp)
REVERT: B  168 CYS cc_start: 0.9010 (m) cc_final: 0.8642 (m)
REVERT: B  204 PHE cc_start: 0.8135 (t80) cc_final: 0.7810 (t80)
REVERT: B  312 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7529 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.0792
  time to fit residues: 36.0512
Evaluate side-chains
  269 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.158284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.127928 restraints weight = 21594.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128289 restraints weight = 13777.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129441 restraints weight = 11096.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129875 restraints weight = 8898.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.130509 restraints weight = 7948.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9804  Z= 0.128
  Angle     :  0.650  12.083  13287  Z= 0.328
  Chirality :  0.041   0.187   1478
  Planarity :  0.004   0.048   1642
  Dihedral  :  4.786  25.141   1277
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.25), residues: 1140
  helix:  1.16 (0.17), residues: 837
  sheet:  None (None), residues: 0
  loop : -2.20 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  91 
 TYR   0.020   0.001   TYR B 162 
 PHE   0.024   0.001   PHE D 561 
 TRP   0.035   0.002   TRP A  27 
 HIS   0.006   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9804)
  covalent geometry    : angle       0.64998 (13287)
  hydrogen bonds       : bond        0.04293 (  616)
  hydrogen bonds       : angle       4.21978 ( 1842)

*********************** 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
  327 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  568 LYS cc_start: 0.7503 (tptp) cc_final: 0.6926 (tptp)
REVERT: D  770 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7032 (pttp)
REVERT: C   71 MET cc_start: 0.8127 (mmm) cc_final: 0.7688 (tpt)
REVERT: C   75 PHE cc_start: 0.7791 (m-80) cc_final: 0.7131 (m-80)
REVERT: C   99 PHE cc_start: 0.5993 (m-80) cc_final: 0.5608 (m-80)
REVERT: C  120 VAL cc_start: 0.8530 (t) cc_final: 0.7573 (t)
REVERT: C  121 LEU cc_start: 0.9602 (mt) cc_final: 0.9235 (mt)
REVERT: C  130 GLU cc_start: 0.7983 (tp30) cc_final: 0.7765 (tp30)
REVERT: C  137 GLN cc_start: 0.7569 (mt0) cc_final: 0.7247 (mt0)
REVERT: C  184 TYR cc_start: 0.7696 (t80) cc_final: 0.7429 (t80)
REVERT: C  187 ASP cc_start: 0.6742 (m-30) cc_final: 0.6387 (m-30)
REVERT: A   74 TYR cc_start: 0.7950 (t80) cc_final: 0.7394 (t80)
REVERT: A   93 LEU cc_start: 0.9373 (mm) cc_final: 0.9075 (mm)
REVERT: A  138 THR cc_start: 0.8244 (m) cc_final: 0.8022 (t)
REVERT: A  372 CYS cc_start: 0.8987 (m) cc_final: 0.8636 (m)
REVERT: A  374 GLN cc_start: 0.8550 (mt0) cc_final: 0.8037 (mm-40)
REVERT: A  520 MET cc_start: 0.8737 (mmm) cc_final: 0.8140 (mmm)
REVERT: A  534 ASP cc_start: 0.8355 (t70) cc_final: 0.7928 (t0)
REVERT: A  571 ASP cc_start: 0.8602 (t0) cc_final: 0.8342 (t0)
REVERT: A  614 LYS cc_start: 0.8037 (tttt) cc_final: 0.7676 (mttt)
REVERT: A  652 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8187 (tttt)
REVERT: B    4 GLU cc_start: 0.7069 (pm20) cc_final: 0.6777 (tm-30)
REVERT: B   36 LEU cc_start: 0.8767 (tp) cc_final: 0.8274 (mm)
REVERT: B   81 HIS cc_start: 0.8931 (m-70) cc_final: 0.7968 (m-70)
REVERT: B  142 MET cc_start: 0.6470 (tpp) cc_final: 0.6137 (tpp)
REVERT: B  168 CYS cc_start: 0.8976 (m) cc_final: 0.8604 (m)
REVERT: B  204 PHE cc_start: 0.8148 (t80) cc_final: 0.7861 (t80)
REVERT: B  312 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7561 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.0783
  time to fit residues: 37.5315
Evaluate side-chains
  263 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0570
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 16 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8900

-------------------------------------------------------------------------------
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**
A 123 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.159535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128249 restraints weight = 21296.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.127577 restraints weight = 13833.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.128569 restraints weight = 11314.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128983 restraints weight = 9597.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.129451 restraints weight = 8609.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9804  Z= 0.128
  Angle     :  0.654  11.862  13287  Z= 0.330
  Chirality :  0.041   0.193   1478
  Planarity :  0.004   0.048   1642
  Dihedral  :  4.714  22.750   1277
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.25), residues: 1140
  helix:  1.21 (0.18), residues: 843
  sheet:  None (None), residues: 0
  loop : -2.23 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 321 
 TYR   0.023   0.001   TYR C 165 
 PHE   0.035   0.001   PHE C 176 
 TRP   0.031   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9804)
  covalent geometry    : angle       0.65426 (13287)
  hydrogen bonds       : bond        0.04176 (  616)
  hydrogen bonds       : angle       4.17204 ( 1842)

********************** 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
  321 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 321
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  568 LYS cc_start: 0.7368 (tptp) cc_final: 0.6769 (tptp)
REVERT: D  770 LYS cc_start: 0.7904 (mmtt) cc_final: 0.6776 (ttpp)
REVERT: D  774 LEU cc_start: 0.8925 (mt) cc_final: 0.8704 (mt)
REVERT: C   47 VAL cc_start: 0.6491 (t) cc_final: 0.6056 (t)
REVERT: C   71 MET cc_start: 0.8292 (mmm) cc_final: 0.7818 (tpt)
REVERT: C   75 PHE cc_start: 0.7943 (m-80) cc_final: 0.7190 (m-80)
REVERT: C   91 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6266 (mtm-85)
REVERT: C   99 PHE cc_start: 0.6044 (m-80) cc_final: 0.5702 (m-80)
REVERT: C  120 VAL cc_start: 0.8507 (t) cc_final: 0.7819 (t)
REVERT: C  121 LEU cc_start: 0.9594 (mt) cc_final: 0.9317 (mt)
REVERT: C  137 GLN cc_start: 0.7473 (mt0) cc_final: 0.7099 (mt0)
REVERT: C  184 TYR cc_start: 0.7820 (t80) cc_final: 0.7346 (t80)
REVERT: C  187 ASP cc_start: 0.6409 (m-30) cc_final: 0.6034 (m-30)
REVERT: A   74 TYR cc_start: 0.7972 (t80) cc_final: 0.7440 (t80)
REVERT: A   93 LEU cc_start: 0.9261 (mm) cc_final: 0.8989 (mm)
REVERT: A  138 THR cc_start: 0.8191 (m) cc_final: 0.7976 (t)
REVERT: A  372 CYS cc_start: 0.9022 (m) cc_final: 0.8659 (m)
REVERT: A  374 GLN cc_start: 0.8633 (mt0) cc_final: 0.8095 (mm-40)
REVERT: A  520 MET cc_start: 0.8777 (mmm) cc_final: 0.8137 (mmm)
REVERT: A  534 ASP cc_start: 0.8462 (t70) cc_final: 0.8047 (t0)
REVERT: A  571 ASP cc_start: 0.8642 (t0) cc_final: 0.8328 (t0)
REVERT: A  607 PHE cc_start: 0.8881 (t80) cc_final: 0.8571 (t80)
REVERT: A  614 LYS cc_start: 0.8049 (tttt) cc_final: 0.7559 (mttt)
REVERT: B    4 GLU cc_start: 0.7068 (pm20) cc_final: 0.6738 (tm-30)
REVERT: B   36 LEU cc_start: 0.8723 (tp) cc_final: 0.8165 (mm)
REVERT: B   37 GLN cc_start: 0.8892 (tt0) cc_final: 0.8464 (tt0)
REVERT: B   81 HIS cc_start: 0.8987 (m-70) cc_final: 0.8003 (m-70)
REVERT: B  142 MET cc_start: 0.6486 (tpp) cc_final: 0.6118 (tpp)
REVERT: B  168 CYS cc_start: 0.8959 (m) cc_final: 0.8602 (m)
REVERT: B  181 GLU cc_start: 0.6360 (mp0) cc_final: 0.5830 (pm20)
REVERT: B  204 PHE cc_start: 0.8270 (t80) cc_final: 0.7990 (t80)
REVERT: B  312 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7737 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 321
  average time/residue: 0.0771
  time to fit residues: 36.5125
Evaluate side-chains
  263 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 111 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
D 771 ASN
** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.157713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125709 restraints weight = 21178.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.126256 restraints weight = 13420.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.126977 restraints weight = 10739.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.127337 restraints weight = 9584.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127738 restraints weight = 8520.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.4750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9804  Z= 0.152
  Angle     :  0.674  11.544  13287  Z= 0.344
  Chirality :  0.042   0.197   1478
  Planarity :  0.005   0.105   1642
  Dihedral  :  4.760  23.080   1277
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1140
  helix:  1.25 (0.18), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.26 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG C  91 
 TYR   0.018   0.002   TYR D 782 
 PHE   0.039   0.002   PHE C 176 
 TRP   0.030   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9804)
  covalent geometry    : angle       0.67427 (13287)
  hydrogen bonds       : bond        0.04322 (  616)
  hydrogen bonds       : angle       4.21667 ( 1842)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1560.81 seconds
wall clock time: 27 minutes 38.19 seconds (1658.19 seconds total)