Starting phenix.real_space_refine
on Sat May  2 15:57:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mqm_48534/05_2026/9mqm_48534_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mqm_48534/05_2026/9mqm_48534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mqm_48534/05_2026/9mqm_48534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mqm_48534/05_2026/9mqm_48534.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mqm_48534/05_2026/9mqm_48534_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mqm_48534/05_2026/9mqm_48534_neut.cif"
  }
  resolution = 3.07
  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=   0.001 sd=   0.014
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: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      42      5.16       5
     C    4397      2.51       5
     N    1105      2.21       5
     O    1285      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6830
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 888, 6829
          Classifications: {'peptide': 888}
          Link IDs: {'CIS': 2, 'PTRANS': 32, 'TRANS': 853}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.33, per 1000 atoms: 0.19
  Number of scatterers: 6830
  At special positions: 0
  Unit cell: (72.54, 87.42, 146.01, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     Mg      1     11.99
     O    1285      8.00
     N    1105      7.00
     C    4397      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: 0.40
  Conformation dependent library (CDL) restraints added in 390.1 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      54.4% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 33
    Processing helix  chain 'A' and resid 34 through 42
      removed outlier: 3.584A  pdb=" N   LEU A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 61
    Processing helix  chain 'A' and resid 73 through 82
    Processing helix  chain 'A' and resid 86 through 102
      removed outlier: 5.743A  pdb=" N   VAL A  92 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 132
      removed outlier: 4.762A  pdb=" N   THR A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LEU A 123 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 4.021A  pdb=" N   ALA A 139 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 203
    Processing helix  chain 'A' and resid 247 through 250
      removed outlier: 3.720A  pdb=" N   ALA A 250 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 247 through 250'
    Processing helix  chain 'A' and resid 251 through 257
    Processing helix  chain 'A' and resid 268 through 282
      removed outlier: 4.143A  pdb=" N   TRP A 278 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 299
      removed outlier: 3.546A  pdb=" N   PHE A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 317
      removed outlier: 3.745A  pdb=" N   THR A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 338
    Processing helix  chain 'A' and resid 347 through 354
      removed outlier: 3.706A  pdb=" N   GLY A 353 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 397
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 3.871A  pdb=" N   LYS A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 458
    Processing helix  chain 'A' and resid 488 through 501
      removed outlier: 3.849A  pdb=" N   VAL A 499 " --> pdb=" O   ILE A 495 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASP A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU A 501 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 506
    Processing helix  chain 'A' and resid 525 through 529
    Processing helix  chain 'A' and resid 547 through 556
      removed outlier: 3.626A  pdb=" N   LYS A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 574
    Processing helix  chain 'A' and resid 576 through 581
      removed outlier: 4.096A  pdb=" N   VAL A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 595
      removed outlier: 3.530A  pdb=" N   ASP A 594 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN A 595 " --> pdb=" O   SER A 591 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 590 through 595'
    Processing helix  chain 'A' and resid 600 through 607
      removed outlier: 3.507A  pdb=" N   ALA A 607 " --> pdb=" O   ALA A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 629
      removed outlier: 3.695A  pdb=" N   ALA A 620 " --> pdb=" O   PRO A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 647
      removed outlier: 4.358A  pdb=" N   ALA A 645 " --> pdb=" O   ASN A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 665
      removed outlier: 3.947A  pdb=" N   GLU A 664 " --> pdb=" O   ASP A 660 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   SER A 665 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 660 through 665'
    Processing helix  chain 'A' and resid 676 through 714
      removed outlier: 3.563A  pdb=" N   LYS A 687 " --> pdb=" O   ILE A 683 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 710 " --> pdb=" O   ASN A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 738
    Processing helix  chain 'A' and resid 739 through 744
      Proline residue:  A 742  - end of helix
      No H-bonds generated for 'chain 'A' and resid 739 through 744'
    Processing helix  chain 'A' and resid 747 through 752
      removed outlier: 3.713A  pdb=" N   VAL A 752 " --> pdb=" O   GLU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 767
      removed outlier: 3.602A  pdb=" N   VAL A 762 " --> pdb=" O   ASP A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 787
      removed outlier: 3.836A  pdb=" N   SER A 773 " --> pdb=" O   ILE A 769 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER A 774 " --> pdb=" O   GLY A 770 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE A 776 " --> pdb=" O   THR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 794
      removed outlier: 3.840A  pdb=" N   THR A 792 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 827
      removed outlier: 3.522A  pdb=" N   THR A 826 " --> pdb=" O   MET A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 833
    Processing helix  chain 'A' and resid 845 through 862
    Processing helix  chain 'A' and resid 865 through 871
      removed outlier: 3.827A  pdb=" N   HIS A 869 " --> pdb=" O   THR A 865 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A 871 " --> pdb=" O   PHE A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 906
    Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 164
      removed outlier: 4.724A  pdb=" N   ASN A 152 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 173 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   VAL A 235 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   PHE A 195 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   SER A 237 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ASP A 193 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   SER A 239 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ALA A 191 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   TYR A 241 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ILE A 189 " --> pdb=" O   TYR A 241 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 185 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   LEU A 194 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164
      removed outlier: 4.724A  pdb=" N   ASN A 152 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 173 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   VAL A 235 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   PHE A 195 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   SER A 237 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ASP A 193 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   SER A 239 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ALA A 191 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   TYR A 241 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ILE A 189 " --> pdb=" O   TYR A 241 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 185 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 589
      removed outlier: 6.430A  pdb=" N   ILE A 588 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   PHE A 611 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   ILE A 564 " --> pdb=" O   PHE A 611 " (cutoff:3.500A)
      removed outlier: 9.039A  pdb=" N   ILE A 653 " --> pdb=" O   VAL A 633 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   TYR A 635 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 436
      removed outlier: 6.395A  pdb=" N   VAL A 448 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   GLU A 435 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   SER A 446 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ARG A 508 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE A 510 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   TYR A 537 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   VAL A 512 " --> pdb=" O   MET A 535 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   MET A 535 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR A 476 " --> pdb=" O   MET A 532 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   LEU A 534 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   VAL A 478 " --> pdb=" O   LEU A 534 " (cutoff:3.500A)
      removed outlier: 8.950A  pdb=" N   GLY A 536 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)

    343 hydrogen bonds defined for protein.
    996 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: 1.23

  Time building geometry restraints manager: 0.57 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: 2152
        1.34 -     1.46: 1013
        1.46 -     1.58: 3704
        1.58 -     1.70: 1
        1.70 -     1.82: 78
  Bond restraints: 6948
  Sorted by residual:
  bond pdb=" N   ASP A 263 "
       pdb=" CA  ASP A 263 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.67e+00
  bond pdb=" N   THR A 265 "
       pdb=" CA  THR A 265 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.028 1.29e-02 6.01e+03 4.88e+00
  bond pdb=" N   LYS A 266 "
       pdb=" CA  LYS A 266 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.38e-02 5.25e+03 4.67e+00
  bond pdb=" N   GLU A 262 "
       pdb=" CA  GLU A 262 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.027 1.29e-02 6.01e+03 4.43e+00
  bond pdb=" N   SER A 264 "
       pdb=" CA  SER A 264 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 1.39e-02 5.18e+03 3.71e+00
  ... (remaining 6943 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 9258
        2.49 -     4.97: 124
        4.97 -     7.46: 26
        7.46 -     9.94: 3
        9.94 -    12.43: 4
  Bond angle restraints: 9415
  Sorted by residual:
  angle pdb=" N   THR A 261 "
        pdb=" CA  THR A 261 "
        pdb=" C   THR A 261 "
      ideal   model   delta    sigma   weight residual
     113.19  106.81    6.38 1.19e+00 7.06e-01 2.88e+01
  angle pdb=" CA  PRO A 863 "
        pdb=" N   PRO A 863 "
        pdb=" CD  PRO A 863 "
      ideal   model   delta    sigma   weight residual
     112.00  104.78    7.22 1.40e+00 5.10e-01 2.66e+01
  angle pdb=" CA  ILE A 189 "
        pdb=" CB  ILE A 189 "
        pdb=" CG1 ILE A 189 "
      ideal   model   delta    sigma   weight residual
     110.40  117.52   -7.12 1.70e+00 3.46e-01 1.75e+01
  angle pdb=" CA  PRO A 322 "
        pdb=" N   PRO A 322 "
        pdb=" CD  PRO A 322 "
      ideal   model   delta    sigma   weight residual
     112.00  106.28    5.72 1.40e+00 5.10e-01 1.67e+01
  angle pdb=" C   PRO A 518 "
        pdb=" N   SER A 519 "
        pdb=" CA  SER A 519 "
      ideal   model   delta    sigma   weight residual
     121.80  131.16   -9.36 2.44e+00 1.68e-01 1.47e+01
  ... (remaining 9410 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 3555
       17.54 -    35.08: 502
       35.08 -    52.61: 119
       52.61 -    70.15: 25
       70.15 -    87.69: 10
  Dihedral angle restraints: 4211
    sinusoidal: 1642
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" CA  LEU A 321 "
           pdb=" C   LEU A 321 "
           pdb=" N   PRO A 322 "
           pdb=" CA  PRO A 322 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.80  -35.20     0      5.00e+00 4.00e-02 4.96e+01
  dihedral pdb=" CA  PRO A 863 "
           pdb=" C   PRO A 863 "
           pdb=" N   PHE A 864 "
           pdb=" CA  PHE A 864 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.68   31.32     0      5.00e+00 4.00e-02 3.93e+01
  dihedral pdb=" CA  ILE A 862 "
           pdb=" C   ILE A 862 "
           pdb=" N   PRO A 863 "
           pdb=" CA  PRO A 863 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.03  -26.97     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 4208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1010
       0.067 -    0.134: 119
       0.134 -    0.201: 7
       0.201 -    0.268: 1
       0.268 -    0.335: 2
  Chirality restraints: 1139
  Sorted by residual:
  chirality pdb=" CB  ILE A 862 "
            pdb=" CA  ILE A 862 "
            pdb=" CG1 ILE A 862 "
            pdb=" CG2 ILE A 862 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CA  PRO A 322 "
            pdb=" N   PRO A 322 "
            pdb=" C   PRO A 322 "
            pdb=" CB  PRO A 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  PRO A 863 "
            pdb=" N   PRO A 863 "
            pdb=" C   PRO A 863 "
            pdb=" CB  PRO A 863 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1136 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 321 "   -0.108 5.00e-02 4.00e+02   1.62e-01 4.19e+01
        pdb=" N   PRO A 322 "    0.280 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.092 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 862 "    0.099 5.00e-02 4.00e+02   1.48e-01 3.53e+01
        pdb=" N   PRO A 863 "   -0.257 5.00e-02 4.00e+02
        pdb=" CA  PRO A 863 "    0.081 5.00e-02 4.00e+02
        pdb=" CD  PRO A 863 "    0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 120 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   THR A 120 "    0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 120 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   MET A 121 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 81
        2.55 -     3.14: 5802
        3.14 -     3.73: 10982
        3.73 -     4.31: 14806
        4.31 -     4.90: 23888
  Nonbonded interactions: 55559
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  85 "
            pdb=" O   ILE A  88 "
     model   vdw
     1.967 3.040
  nonbonded pdb=" OD1 ASN A 706 "
            pdb="MG    MG A1001 "
     model   vdw
     1.992 2.170
  nonbonded pdb=" OG  SER A 530 "
            pdb=" OE1 GLU A 531 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" O   LYS A 498 "
            pdb=" N   ASP A 500 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OG  SER A  50 "
            pdb=" OE1 GLN A  53 "
     model   vdw
     2.239 3.040
  ... (remaining 55554 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.740
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
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      :  0.004   0.096   6948  Z= 0.169
  Angle     :  0.741  12.427   9415  Z= 0.393
  Chirality :  0.046   0.335   1139
  Planarity :  0.007   0.162   1175
  Dihedral  : 17.447  87.691   2547
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  1.13 %
    Allowed  :  8.35 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 32.37 %
    Favored  : 65.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    Twisted General : 0.12 %

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: -0.47 (0.29), residues: 886
  helix:  0.84 (0.27), residues: 385
  sheet: -0.17 (0.61), residues: 72
  loop : -1.44 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 444 
 TYR   0.006   0.001   TYR A 906 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.006   0.001   TRP A 743 
 HIS   0.001   0.000   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6948)
  covalent geometry    : angle       0.74115 ( 9415)
  hydrogen bonds       : bond        0.23297 (  328)
  hydrogen bonds       : angle       7.67664 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8516 (m-30) cc_final: 0.8311 (m-30)
REVERT: A  290 PHE cc_start: 0.8741 (t80) cc_final: 0.8449 (t80)
REVERT: A  374 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7095 (mmm)
REVERT: A  571 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8331 (mmmm)
REVERT: A  893 MET cc_start: 0.8728 (mtp) cc_final: 0.8321 (tmm)
  outliers start: 16
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0678
  time to fit residues: 8.4061
Evaluate side-chains
  81 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  650 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  834 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 274 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 350 GLN
A 356 ASN
A 380 HIS
A 452 ASN
A 454 ASN
A 628 ASN
A 841 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.097588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.063956 restraints weight = 15387.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 3.28
r_work: 0.2899 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   6948  Z= 0.154
  Angle     :  0.712  13.332   9415  Z= 0.364
  Chirality :  0.047   0.370   1139
  Planarity :  0.008   0.164   1175
  Dihedral  :  6.084  37.978    947
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.11 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 29.62 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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: -0.23 (0.29), residues: 886
  helix:  1.00 (0.26), residues: 430
  sheet: -0.10 (0.58), residues: 77
  loop : -1.54 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 187 
 TYR   0.010   0.001   TYR A 397 
 PHE   0.021   0.001   PHE A 776 
 TRP   0.007   0.001   TRP A 817 
 HIS   0.002   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6948)
  covalent geometry    : angle       0.71203 ( 9415)
  hydrogen bonds       : bond        0.05045 (  328)
  hydrogen bonds       : angle       5.29716 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  454 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8927 (t0)
  outliers start: 33
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0596
  time to fit residues: 8.8047
Evaluate side-chains
  78 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  256 MET
Chi-restraints excluded: chain A residue  454 ASN
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  712 ILE
Chi-restraints excluded: chain A residue  738 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 83 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.064199 restraints weight = 15268.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 3.28
r_work: 0.2907 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   6948  Z= 0.147
  Angle     :  0.696  13.255   9415  Z= 0.352
  Chirality :  0.047   0.429   1139
  Planarity :  0.008   0.163   1175
  Dihedral  :  5.049  36.871    929
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.45 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 29.49 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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: -0.18 (0.29), residues: 886
  helix:  1.07 (0.26), residues: 432
  sheet: -0.24 (0.57), residues: 77
  loop : -1.53 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 187 
 TYR   0.010   0.001   TYR A 397 
 PHE   0.017   0.001   PHE A 776 
 TRP   0.007   0.001   TRP A 817 
 HIS   0.001   0.000   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6948)
  covalent geometry    : angle       0.69554 ( 9415)
  hydrogen bonds       : bond        0.04444 (  328)
  hydrogen bonds       : angle       5.02905 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8570 (p90)
  outliers start: 27
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0588
  time to fit residues: 8.4635
Evaluate side-chains
  87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  376 HIS
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  738 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.097228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.063981 restraints weight = 15503.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 3.27
r_work: 0.2894 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   6948  Z= 0.153
  Angle     :  0.699  13.242   9415  Z= 0.352
  Chirality :  0.047   0.436   1139
  Planarity :  0.008   0.164   1175
  Dihedral  :  5.047  36.724    929
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.56 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 29.49 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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: -0.09 (0.29), residues: 886
  helix:  1.10 (0.26), residues: 432
  sheet: -0.06 (0.55), residues: 89
  loop : -1.50 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  77 
 TYR   0.011   0.001   TYR A 397 
 PHE   0.018   0.001   PHE A 776 
 TRP   0.008   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6948)
  covalent geometry    : angle       0.69854 ( 9415)
  hydrogen bonds       : bond        0.04194 (  328)
  hydrogen bonds       : angle       4.86490 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8544 (m-30) cc_final: 0.8242 (m-30)
REVERT: A  376 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8577 (p90)
  outliers start: 27
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0537
  time to fit residues: 7.8712
Evaluate side-chains
  88 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  376 HIS
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  738 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0070
   chunk 6 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0370
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 347 ASN
A 830 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.100133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.068333 restraints weight = 15425.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 3.20
r_work: 0.2951 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.113   6948  Z= 0.125
  Angle     :  0.681  12.866   9415  Z= 0.340
  Chirality :  0.047   0.469   1139
  Planarity :  0.007   0.162   1175
  Dihedral  :  4.936  37.039    929
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.56 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 28.57 %
    Favored  : 67.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.03 (0.29), residues: 886
  helix:  1.21 (0.26), residues: 430
  sheet:  0.14 (0.62), residues: 77
  loop : -1.43 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 686 
 TYR   0.011   0.001   TYR A 397 
 PHE   0.016   0.001   PHE A 776 
 TRP   0.009   0.001   TRP A 817 
 HIS   0.002   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6948)
  covalent geometry    : angle       0.68079 ( 9415)
  hydrogen bonds       : bond        0.03615 (  328)
  hydrogen bonds       : angle       4.67473 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 MET cc_start: 0.7531 (mmm) cc_final: 0.7225 (mmm)
REVERT: A  376 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8565 (p90)
REVERT: A  406 ASP cc_start: 0.9058 (m-30) cc_final: 0.8622 (m-30)
  outliers start: 28
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0598
  time to fit residues: 9.0588
Evaluate side-chains
  90 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  376 HIS
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  803 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0570
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.098524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.065474 restraints weight = 15392.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 3.26
r_work: 0.2928 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   6948  Z= 0.134
  Angle     :  0.685  12.845   9415  Z= 0.345
  Chirality :  0.047   0.466   1139
  Planarity :  0.008   0.162   1175
  Dihedral  :  4.895  36.663    929
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.56 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 30.01 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.06 (0.29), residues: 886
  helix:  1.26 (0.26), residues: 431
  sheet:  0.12 (0.62), residues: 77
  loop : -1.45 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 686 
 TYR   0.013   0.001   TYR A  79 
 PHE   0.016   0.001   PHE A 776 
 TRP   0.008   0.001   TRP A 278 
 HIS   0.003   0.000   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6948)
  covalent geometry    : angle       0.68496 ( 9415)
  hydrogen bonds       : bond        0.03606 (  328)
  hydrogen bonds       : angle       4.60392 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 ASP cc_start: 0.9063 (m-30) cc_final: 0.8622 (m-30)
REVERT: A  541 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7719 (pt)
  outliers start: 20
  outliers final: 13
  residues processed: 94
  average time/residue: 0.0563
  time to fit residues: 7.9973
Evaluate side-chains
  87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  803 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 46 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
A 368 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.098576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.065032 restraints weight = 15267.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 3.29
r_work: 0.2920 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   6948  Z= 0.136
  Angle     :  0.692  12.757   9415  Z= 0.347
  Chirality :  0.047   0.461   1139
  Planarity :  0.008   0.162   1175
  Dihedral  :  4.892  36.536    929
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  1.13 %
    Allowed  :  7.45 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 29.62 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.12 (0.30), residues: 886
  helix:  1.33 (0.26), residues: 429
  sheet:  0.09 (0.62), residues: 77
  loop : -1.42 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 686 
 TYR   0.014   0.001   TYR A  79 
 PHE   0.017   0.001   PHE A 776 
 TRP   0.010   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6948)
  covalent geometry    : angle       0.69222 ( 9415)
  hydrogen bonds       : bond        0.03602 (  328)
  hydrogen bonds       : angle       4.56783 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 ASP cc_start: 0.9070 (m-30) cc_final: 0.8626 (m-30)
  outliers start: 23
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0605
  time to fit residues: 8.5148
Evaluate side-chains
  87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  803 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.064584 restraints weight = 15444.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 3.25
r_work: 0.2906 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   6948  Z= 0.148
  Angle     :  0.705  12.814   9415  Z= 0.354
  Chirality :  0.047   0.463   1139
  Planarity :  0.008   0.162   1175
  Dihedral  :  4.924  36.685    929
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  1.13 %
    Allowed  :  7.56 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 29.75 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.11 (0.29), residues: 886
  helix:  1.34 (0.26), residues: 429
  sheet:  0.10 (0.68), residues: 65
  loop : -1.40 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 686 
 TYR   0.009   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 776 
 TRP   0.010   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6948)
  covalent geometry    : angle       0.70453 ( 9415)
  hydrogen bonds       : bond        0.03689 (  328)
  hydrogen bonds       : angle       4.55923 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 GLU cc_start: 0.9127 (mp0) cc_final: 0.8895 (mp0)
REVERT: A  406 ASP cc_start: 0.9059 (m-30) cc_final: 0.8630 (m-30)
  outliers start: 22
  outliers final: 15
  residues processed: 91
  average time/residue: 0.0583
  time to fit residues: 7.9832
Evaluate side-chains
  86 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  803 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0060
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0370
   chunk 15 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.3652

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.099584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.066287 restraints weight = 15486.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.33
r_work: 0.2944 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.111   6948  Z= 0.126
  Angle     :  0.694  12.732   9415  Z= 0.347
  Chirality :  0.046   0.447   1139
  Planarity :  0.007   0.161   1175
  Dihedral  :  4.859  37.237    929
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  :  7.11 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 30.67 %
    Favored  : 67.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.18 (0.30), residues: 886
  helix:  1.37 (0.26), residues: 430
  sheet:  0.12 (0.68), residues: 65
  loop : -1.34 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 686 
 TYR   0.010   0.001   TYR A 397 
 PHE   0.023   0.001   PHE A 524 
 TRP   0.011   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6948)
  covalent geometry    : angle       0.69408 ( 9415)
  hydrogen bonds       : bond        0.03337 (  328)
  hydrogen bonds       : angle       4.50822 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8612 (m-30) cc_final: 0.8405 (m-30)
REVERT: A  303 MET cc_start: 0.8535 (tpp) cc_final: 0.8334 (tpp)
REVERT: A  406 ASP cc_start: 0.9049 (m-30) cc_final: 0.8612 (m-30)
  outliers start: 17
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0604
  time to fit residues: 8.0145
Evaluate side-chains
  82 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  803 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 39 optimal weight:    0.0980
   chunk 49 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.098653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.065248 restraints weight = 15518.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.32
r_work: 0.2924 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.106   6948  Z= 0.137
  Angle     :  0.701  12.787   9415  Z= 0.351
  Chirality :  0.047   0.436   1139
  Planarity :  0.008   0.161   1175
  Dihedral  :  4.867  37.238    929
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  :  7.22 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 30.93 %
    Favored  : 67.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.24 (0.30), residues: 886
  helix:  1.41 (0.26), residues: 429
  sheet:  0.03 (0.62), residues: 77
  loop : -1.30 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 686 
 TYR   0.009   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 524 
 TRP   0.010   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6948)
  covalent geometry    : angle       0.70062 ( 9415)
  hydrogen bonds       : bond        0.03493 (  328)
  hydrogen bonds       : angle       4.48863 (  996)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8623 (m-30) cc_final: 0.8415 (m-30)
REVERT: A  541 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7624 (pt)
  outliers start: 15
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0582
  time to fit residues: 7.2820
Evaluate side-chains
  82 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  738 CYS
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  803 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.098644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.065265 restraints weight = 15417.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.30
r_work: 0.2925 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.107   6948  Z= 0.136
  Angle     :  0.696  12.831   9415  Z= 0.350
  Chirality :  0.047   0.441   1139
  Planarity :  0.007   0.161   1175
  Dihedral  :  4.853  37.063    929
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  :  7.56 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 30.67 %
    Favored  : 67.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.23 %
    Twisted Proline : 3.12 %
    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:  0.25 (0.30), residues: 886
  helix:  1.42 (0.26), residues: 429
  sheet:  0.13 (0.69), residues: 65
  loop : -1.29 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 686 
 TYR   0.009   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 524 
 TRP   0.011   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6948)
  covalent geometry    : angle       0.69593 ( 9415)
  hydrogen bonds       : bond        0.03470 (  328)
  hydrogen bonds       : angle       4.48805 (  996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1687.80 seconds
wall clock time: 29 minutes 46.91 seconds (1786.91 seconds total)