Starting phenix.real_space_refine
on Wed Feb 12 00:53:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwp_35776/02_2025/8iwp_35776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwp_35776/02_2025/8iwp_35776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwp_35776/02_2025/8iwp_35776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwp_35776/02_2025/8iwp_35776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwp_35776/02_2025/8iwp_35776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwp_35776/02_2025/8iwp_35776.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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
     Ca      1      9.91       5
     S      52      5.16       5
     C    4372      2.51       5
     N    1147      2.21       5
     O    1289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6861
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 896, 6860
          Classifications: {'peptide': 896}
          Link IDs: {'PTRANS': 35, 'TRANS': 860}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.80, per 1000 atoms: 0.70
  Number of scatterers: 6861
  At special positions: 0
  Unit cell: (86.52, 99.96, 134.4, 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)
     Ca      1     19.99
     S      52     16.00
     O    1289      8.00
     N    1147      7.00
     C    4372      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: 1.62
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      54.4% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 29
    Processing helix  chain 'A' and resid 30 through 39
    Processing helix  chain 'A' and resid 47 through 58
    Processing helix  chain 'A' and resid 70 through 78
      removed outlier: 3.645A  pdb=" N   LYS A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 97
    Processing helix  chain 'A' and resid 99 through 131
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 256 through 287
      removed outlier: 3.648A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 305
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 334 through 341
      removed outlier: 3.601A  pdb=" N   ILE A 337 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 338 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 411
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 4.006A  pdb=" N   MET A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 5.529A  pdb=" N   GLY A 441 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLN A 443 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 487
    Processing helix  chain 'A' and resid 503 through 520
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 573 through 585
    Processing helix  chain 'A' and resid 596 through 602
    Processing helix  chain 'A' and resid 610 through 612
      No H-bonds generated for 'chain 'A' and resid 610 through 612'
    Processing helix  chain 'A' and resid 621 through 636
      removed outlier: 3.736A  pdb=" N   ASN A 635 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A 636 " --> pdb=" O   LEU A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 654
    Processing helix  chain 'A' and resid 667 through 672
    Processing helix  chain 'A' and resid 683 through 723
      removed outlier: 4.203A  pdb=" N   SER A 687 " --> pdb=" O   GLN A 683 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A 688 " --> pdb=" O   THR A 684 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   MET A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 742
    Processing helix  chain 'A' and resid 743 through 751
    Processing helix  chain 'A' and resid 757 through 761
      removed outlier: 3.526A  pdb=" N   ARG A 760 " --> pdb=" O   ASP A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 798
    Processing helix  chain 'A' and resid 804 through 826
      removed outlier: 4.279A  pdb=" N   THR A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 837
      removed outlier: 3.709A  pdb=" N   ILE A 836 " --> pdb=" O   SER A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 861
    Processing helix  chain 'A' and resid 861 through 869
    Processing helix  chain 'A' and resid 874 through 885
    Processing helix  chain 'A' and resid 888 through 910
    Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151
      removed outlier: 3.550A  pdb=" N   THR A 150 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   CYS A 139 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LEU A 181 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE A 183 " --> pdb=" O   CYS A 195 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   CYS A 195 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151
      removed outlier: 3.550A  pdb=" N   THR A 150 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   CYS A 139 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350
      removed outlier: 6.629A  pdb=" N   GLN A 592 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   VAL A 616 " --> pdb=" O   GLN A 592 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A 594 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR A 618 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392
      removed outlier: 5.040A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE A 545 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS A 364 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   PHE A 538 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   SER A 529 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY A 540 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 463 " --> pdb=" O   PHE A 478 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS A 480 " --> pdb=" O   MET A 461 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ALA A 462 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   GLU A 451 " --> pdb=" O   ALA A 462 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS A 464 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392
      removed outlier: 5.040A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE A 545 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS A 364 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   PHE A 538 " --> pdb=" O   CYS A 490 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   THR A 492 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   GLY A 540 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
      removed outlier: 10.699A  pdb=" N   GLN A 494 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 14.335A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417
      removed outlier: 4.370A  pdb=" N   VAL A 415 " --> pdb=" O   MET A 422 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   MET A 422 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 661
      removed outlier: 6.517A  pdb=" N   ALA A 660 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    412 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.45

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2230
        1.34 -     1.46: 1366
        1.46 -     1.58: 3290
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 6970
  Sorted by residual:
  bond pdb=" CA  GLU A  62 "
       pdb=" CB  GLU A  62 "
    ideal  model  delta    sigma   weight residual
    1.535  1.562 -0.027 1.58e-02 4.01e+03 2.98e+00
  bond pdb=" CB  PRO A 744 "
       pdb=" CG  PRO A 744 "
    ideal  model  delta    sigma   weight residual
    1.492  1.578 -0.086 5.00e-02 4.00e+02 2.94e+00
  bond pdb=" CA  THR A 590 "
       pdb=" CB  THR A 590 "
    ideal  model  delta    sigma   weight residual
    1.528  1.565 -0.037 2.61e-02 1.47e+03 1.99e+00
  bond pdb=" CG1 ILE A 431 "
       pdb=" CD1 ILE A 431 "
    ideal  model  delta    sigma   weight residual
    1.513  1.462  0.051 3.90e-02 6.57e+02 1.68e+00
  bond pdb=" C   THR A 804 "
       pdb=" N   PRO A 805 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.57e+00
  ... (remaining 6965 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 9254
        2.04 -     4.09: 134
        4.09 -     6.13: 35
        6.13 -     8.17: 11
        8.17 -    10.21: 4
  Bond angle restraints: 9438
  Sorted by residual:
  angle pdb=" CA  PRO A 744 "
        pdb=" N   PRO A 744 "
        pdb=" CD  PRO A 744 "
      ideal   model   delta    sigma   weight residual
     112.00  106.71    5.29 1.40e+00 5.10e-01 1.43e+01
  angle pdb=" CA  GLN A 512 "
        pdb=" CB  GLN A 512 "
        pdb=" CG  GLN A 512 "
      ideal   model   delta    sigma   weight residual
     114.10  121.37   -7.27 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" CB  LYS A 756 "
        pdb=" CG  LYS A 756 "
        pdb=" CD  LYS A 756 "
      ideal   model   delta    sigma   weight residual
     111.30  118.84   -7.54 2.30e+00 1.89e-01 1.08e+01
  angle pdb=" CA  LYS A 424 "
        pdb=" CB  LYS A 424 "
        pdb=" CG  LYS A 424 "
      ideal   model   delta    sigma   weight residual
     114.10  120.66   -6.56 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" C   VAL A 346 "
        pdb=" CA  VAL A 346 "
        pdb=" CB  VAL A 346 "
      ideal   model   delta    sigma   weight residual
     111.29  116.55   -5.26 1.64e+00 3.72e-01 1.03e+01
  ... (remaining 9433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3711
       17.97 -    35.93: 422
       35.93 -    53.90: 100
       53.90 -    71.87: 21
       71.87 -    89.84: 7
  Dihedral angle restraints: 4261
    sinusoidal: 1680
      harmonic: 2581
  Sorted by residual:
  dihedral pdb=" CA  ASN A  81 "
           pdb=" C   ASN A  81 "
           pdb=" N   PRO A  82 "
           pdb=" CA  PRO A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.52  -27.48     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  MET A 602 "
           pdb=" C   MET A 602 "
           pdb=" N   ASP A 603 "
           pdb=" CA  ASP A 603 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.17  -23.83     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  GLY A 208 "
           pdb=" C   GLY A 208 "
           pdb=" N   ASP A 209 "
           pdb=" CA  ASP A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 4258 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 829
       0.039 -    0.078: 219
       0.078 -    0.116: 78
       0.116 -    0.155: 6
       0.155 -    0.194: 3
  Chirality restraints: 1135
  Sorted by residual:
  chirality pdb=" CG  LEU A 780 "
            pdb=" CB  LEU A 780 "
            pdb=" CD1 LEU A 780 "
            pdb=" CD2 LEU A 780 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.40e-01
  chirality pdb=" CA  THR A 804 "
            pdb=" N   THR A 804 "
            pdb=" C   THR A 804 "
            pdb=" CB  THR A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 9.01e-01
  chirality pdb=" CG  LEU A  29 "
            pdb=" CB  LEU A  29 "
            pdb=" CD1 LEU A  29 "
            pdb=" CD2 LEU A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.18e-01
  ... (remaining 1132 not shown)

  Planarity restraints: 1193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 743 "   -0.079 5.00e-02 4.00e+02   1.17e-01 2.20e+01
        pdb=" N   PRO A 744 "    0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO A 744 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 744 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  60 "    0.014 2.00e-02 2.50e+03   1.54e-02 5.93e+00
        pdb=" CG  TRP A  60 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  60 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  60 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  60 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  72 "   -0.013 2.00e-02 2.50e+03   1.17e-02 3.43e+00
        pdb=" CG  TRP A  72 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  72 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  72 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  72 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  72 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  72 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  72 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1190 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2013
        2.82 -     3.34: 6677
        3.34 -     3.86: 11234
        3.86 -     4.38: 11909
        4.38 -     4.90: 21428
  Nonbonded interactions: 53261
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 570 "
            pdb=" OD2 ASP A 572 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" N   GLN A 829 "
            pdb=" OE1 GLN A 829 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" NZ  LYS A 333 "
            pdb=" O   ALA A 673 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" ND2 ASN A  61 "
            pdb=" O   ALA A 152 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" N   THR A 503 "
            pdb=" OE1 GLN A 506 "
     model   vdw
     2.362 3.120
  ... (remaining 53256 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 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:             2.990
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.500
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
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      :  0.003   0.086   6970  Z= 0.204
  Angle     :  0.688  10.214   9438  Z= 0.365
  Chirality :  0.041   0.194   1135
  Planarity :  0.005   0.117   1193
  Dihedral  : 16.146  89.836   2591
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.92 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 25.03 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.30), residues: 894
  helix:  2.02 (0.24), residues: 461
  sheet: -0.49 (0.56), residues: 99
  loop : -0.19 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A  60 
 HIS   0.002   0.000   HIS A 149 
 PHE   0.020   0.001   PHE A 241 
 TYR   0.010   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 403 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   71 LEU cc_start: 0.7714 (pp) cc_final: 0.7415 (pp)
REVERT: A  797 GLU cc_start: 0.6317 (tm-30) cc_final: 0.5636 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 134
  average time/residue: 0.1791
  time to fit residues: 33.4028
Evaluate side-chains
  132 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  739 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    0.1980
   chunk 36 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 683 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.202305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156381 restraints weight = 9048.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.157976 restraints weight = 7051.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.159942 restraints weight = 5578.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6970  Z= 0.229
  Angle     :  0.615   8.375   9438  Z= 0.309
  Chirality :  0.042   0.208   1135
  Planarity :  0.004   0.075   1193
  Dihedral  :  4.607  58.549    950
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.03 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.27 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.29), residues: 894
  helix:  2.10 (0.24), residues: 461
  sheet:  0.32 (0.61), residues: 76
  loop : -0.40 (0.36), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  60 
 HIS   0.005   0.001   HIS A 149 
 PHE   0.012   0.001   PHE A 812 
 TYR   0.011   0.001   TYR A 483 
 ARG   0.003   0.000   ARG A 174 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  306 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (mt)
REVERT: A  435 MET cc_start: 0.7224 (tmm) cc_final: 0.6704 (tmm)
REVERT: A  780 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8490 (mm)
  outliers start: 22
  outliers final: 11
  residues processed: 146
  average time/residue: 0.1703
  time to fit residues: 34.3500
Evaluate side-chains
  131 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  790 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0070
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.6006

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.190982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.144626 restraints weight = 9547.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.141633 restraints weight = 10142.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143883 restraints weight = 9440.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   6970  Z= 0.428
  Angle     :  0.757  10.108   9438  Z= 0.384
  Chirality :  0.046   0.226   1135
  Planarity :  0.005   0.070   1193
  Dihedral  :  4.686  28.862    946
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.81 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 20.88 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.29), residues: 894
  helix:  1.57 (0.24), residues: 463
  sheet: -0.09 (0.66), residues: 73
  loop : -0.46 (0.36), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  60 
 HIS   0.005   0.001   HIS A  58 
 PHE   0.020   0.002   PHE A 725 
 TYR   0.015   0.002   TYR A 618 
 ARG   0.007   0.001   ARG A  55 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8146 (tp30) cc_final: 0.7891 (tt0)
REVERT: A  281 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7806 (tmt)
REVERT: A  306 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8821 (mt)
REVERT: A  312 ILE cc_start: 0.8958 (mm) cc_final: 0.8743 (mt)
REVERT: A  435 MET cc_start: 0.7329 (tmm) cc_final: 0.6794 (tmm)
REVERT: A  648 ASP cc_start: 0.7248 (m-30) cc_final: 0.7048 (m-30)
REVERT: A  679 ASP cc_start: 0.8427 (t0) cc_final: 0.7877 (t70)
REVERT: A  757 ASP cc_start: 0.8395 (t0) cc_final: 0.8176 (t70)
REVERT: A  780 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8400 (mm)
  outliers start: 40
  outliers final: 24
  residues processed: 154
  average time/residue: 0.1723
  time to fit residues: 36.4855
Evaluate side-chains
  150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  898 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 494 GLN
A 855 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.193194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.147631 restraints weight = 9553.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146437 restraints weight = 9286.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148347 restraints weight = 8569.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6970  Z= 0.225
  Angle     :  0.636   9.585   9438  Z= 0.318
  Chirality :  0.042   0.202   1135
  Planarity :  0.004   0.064   1193
  Dihedral  :  4.439  29.342    946
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.81 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.57 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.29), residues: 894
  helix:  1.88 (0.24), residues: 464
  sheet: -0.20 (0.66), residues: 73
  loop : -0.44 (0.36), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  72 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.016   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 174 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8068 (tp30) cc_final: 0.7867 (tt0)
REVERT: A  281 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7766 (tmt)
REVERT: A  306 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8850 (mt)
REVERT: A  312 ILE cc_start: 0.8888 (mm) cc_final: 0.8663 (mt)
REVERT: A  435 MET cc_start: 0.7504 (tmm) cc_final: 0.6930 (tmm)
REVERT: A  594 VAL cc_start: 0.8397 (t) cc_final: 0.8177 (t)
REVERT: A  757 ASP cc_start: 0.8270 (t0) cc_final: 0.8018 (t0)
REVERT: A  780 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8341 (mm)
  outliers start: 29
  outliers final: 20
  residues processed: 142
  average time/residue: 0.1789
  time to fit residues: 34.5972
Evaluate side-chains
  140 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 80 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.191654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.148800 restraints weight = 9251.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.145065 restraints weight = 10257.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.147616 restraints weight = 9408.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6970  Z= 0.250
  Angle     :  0.662  12.097   9438  Z= 0.326
  Chirality :  0.043   0.208   1135
  Planarity :  0.004   0.061   1193
  Dihedral  :  4.471  33.664    946
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.36 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 23.35 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.30), residues: 894
  helix:  1.88 (0.24), residues: 464
  sheet: -0.79 (0.63), residues: 79
  loop : -0.31 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A  72 
 HIS   0.002   0.001   HIS A  58 
 PHE   0.015   0.002   PHE A 702 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 796 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7721 (tmt)
REVERT: A  312 ILE cc_start: 0.8930 (mm) cc_final: 0.8687 (mt)
REVERT: A  435 MET cc_start: 0.7563 (tmm) cc_final: 0.6934 (tmm)
REVERT: A  479 MET cc_start: 0.5146 (tpt) cc_final: 0.4559 (tmm)
REVERT: A  613 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8278 (ttpp)
REVERT: A  679 ASP cc_start: 0.8283 (t0) cc_final: 0.7950 (t70)
REVERT: A  780 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8361 (mm)
  outliers start: 35
  outliers final: 28
  residues processed: 139
  average time/residue: 0.1930
  time to fit residues: 36.1166
Evaluate side-chains
  147 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 68 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:   20.0000
   chunk 66 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 75 optimal weight:    0.3980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.193720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147137 restraints weight = 9381.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.147291 restraints weight = 8215.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.149613 restraints weight = 7292.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6970  Z= 0.197
  Angle     :  0.630  11.080   9438  Z= 0.311
  Chirality :  0.042   0.198   1135
  Planarity :  0.004   0.058   1193
  Dihedral  :  4.351  32.440    946
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.92 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 22.70 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.30), residues: 894
  helix:  1.94 (0.24), residues: 470
  sheet: -0.20 (0.66), residues: 72
  loop : -0.32 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  72 
 HIS   0.002   0.000   HIS A 149 
 PHE   0.014   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.004   0.000   ARG A 523 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8809 (mt)
REVERT: A  312 ILE cc_start: 0.8868 (mm) cc_final: 0.8619 (mt)
REVERT: A  435 MET cc_start: 0.7617 (tmm) cc_final: 0.6998 (tmm)
REVERT: A  594 VAL cc_start: 0.8404 (t) cc_final: 0.8137 (t)
REVERT: A  613 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8241 (ttpp)
REVERT: A  679 ASP cc_start: 0.8252 (t0) cc_final: 0.7829 (t70)
REVERT: A  780 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8363 (mm)
  outliers start: 35
  outliers final: 24
  residues processed: 145
  average time/residue: 0.1786
  time to fit residues: 35.6933
Evaluate side-chains
  144 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   78 GLN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0970
   chunk 53 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.193070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.148826 restraints weight = 9199.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.148562 restraints weight = 9204.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.150165 restraints weight = 8817.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6970  Z= 0.240
  Angle     :  0.657  11.410   9438  Z= 0.326
  Chirality :  0.042   0.201   1135
  Planarity :  0.004   0.056   1193
  Dihedral  :  4.477  34.596    946
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.81 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 23.09 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.30), residues: 894
  helix:  1.94 (0.24), residues: 470
  sheet: -0.64 (0.64), residues: 77
  loop : -0.26 (0.37), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  72 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.013   0.001   PHE A 725 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 523 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7745 (tmt)
REVERT: A  306 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8815 (mt)
REVERT: A  312 ILE cc_start: 0.8898 (mm) cc_final: 0.8659 (mt)
REVERT: A  435 MET cc_start: 0.7680 (tmm) cc_final: 0.7037 (tmm)
REVERT: A  613 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8242 (ttpp)
REVERT: A  679 ASP cc_start: 0.8342 (t0) cc_final: 0.7939 (t70)
REVERT: A  780 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8268 (mm)
  outliers start: 39
  outliers final: 33
  residues processed: 145
  average time/residue: 0.1712
  time to fit residues: 34.1394
Evaluate side-chains
  158 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   78 GLN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 32 optimal weight:    0.0470
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 149 HIS
A 467 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.193346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.149446 restraints weight = 9314.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.145794 restraints weight = 8168.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148062 restraints weight = 8847.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6970  Z= 0.228
  Angle     :  0.650  11.339   9438  Z= 0.322
  Chirality :  0.042   0.200   1135
  Planarity :  0.004   0.055   1193
  Dihedral  :  4.514  35.963    946
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 23.48 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.30), residues: 894
  helix:  1.97 (0.24), residues: 470
  sheet: -0.22 (0.67), residues: 71
  loop : -0.39 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  72 
 HIS   0.003   0.000   HIS A  58 
 PHE   0.014   0.001   PHE A 702 
 TYR   0.015   0.001   TYR A 380 
 ARG   0.003   0.000   ARG A 523 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8821 (mt)
REVERT: A  312 ILE cc_start: 0.8908 (mm) cc_final: 0.8663 (mt)
REVERT: A  435 MET cc_start: 0.7688 (tmm) cc_final: 0.7049 (tmm)
REVERT: A  613 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8242 (ttpp)
REVERT: A  679 ASP cc_start: 0.8369 (t0) cc_final: 0.7972 (t70)
REVERT: A  780 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8297 (mm)
  outliers start: 41
  outliers final: 35
  residues processed: 149
  average time/residue: 0.1775
  time to fit residues: 35.9938
Evaluate side-chains
  159 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   78 GLN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LYS
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 74 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.192499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.149214 restraints weight = 9329.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148009 restraints weight = 10365.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150118 restraints weight = 9230.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6970  Z= 0.239
  Angle     :  0.664  11.222   9438  Z= 0.328
  Chirality :  0.042   0.199   1135
  Planarity :  0.004   0.055   1193
  Dihedral  :  4.555  37.534    946
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 23.74 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.30), residues: 894
  helix:  1.95 (0.24), residues: 470
  sheet: -0.71 (0.64), residues: 77
  loop : -0.32 (0.37), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  72 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.013   0.001   PHE A 702 
 TYR   0.020   0.001   TYR A 483 
 ARG   0.003   0.000   ARG A 523 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 ARG cc_start: 0.4970 (mtm180) cc_final: 0.4671 (mtm180)
REVERT: A  306 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8824 (mt)
REVERT: A  312 ILE cc_start: 0.8937 (mm) cc_final: 0.8695 (mt)
REVERT: A  435 MET cc_start: 0.7592 (tmm) cc_final: 0.6979 (tmm)
REVERT: A  679 ASP cc_start: 0.8384 (t0) cc_final: 0.8018 (t70)
REVERT: A  780 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8318 (mm)
REVERT: A  900 ARG cc_start: 0.6418 (ptt180) cc_final: 0.6135 (ptt180)
  outliers start: 39
  outliers final: 35
  residues processed: 148
  average time/residue: 0.1727
  time to fit residues: 35.0279
Evaluate side-chains
  160 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   78 GLN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 149 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.190777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.146947 restraints weight = 9426.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143764 restraints weight = 10135.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.146123 restraints weight = 9334.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6970  Z= 0.297
  Angle     :  0.720  11.874   9438  Z= 0.355
  Chirality :  0.043   0.208   1135
  Planarity :  0.004   0.054   1193
  Dihedral  :  4.728  42.858    946
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.99 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.30), residues: 894
  helix:  1.87 (0.24), residues: 470
  sheet: -0.85 (0.62), residues: 76
  loop : -0.29 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.016   0.002   PHE A 725 
 TYR   0.019   0.002   TYR A 483 
 ARG   0.003   0.000   ARG A 523 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 ARG cc_start: 0.4848 (mtm180) cc_final: 0.4316 (ttm170)
REVERT: A  281 MET cc_start: 0.8205 (tmm) cc_final: 0.7837 (tmt)
REVERT: A  306 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8795 (mt)
REVERT: A  312 ILE cc_start: 0.8997 (mm) cc_final: 0.8752 (mt)
REVERT: A  435 MET cc_start: 0.7631 (tmm) cc_final: 0.6989 (tmm)
REVERT: A  679 ASP cc_start: 0.8489 (t0) cc_final: 0.8104 (t70)
REVERT: A  780 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8351 (mm)
  outliers start: 38
  outliers final: 31
  residues processed: 147
  average time/residue: 0.1836
  time to fit residues: 36.7125
Evaluate side-chains
  156 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   78 GLN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 149 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.192449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.149087 restraints weight = 9315.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.147267 restraints weight = 9837.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.149791 restraints weight = 9206.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6970  Z= 0.247
  Angle     :  0.711  11.878   9438  Z= 0.348
  Chirality :  0.043   0.200   1135
  Planarity :  0.004   0.054   1193
  Dihedral  :  4.682  43.551    946
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 24.12 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.30), residues: 894
  helix:  1.93 (0.24), residues: 469
  sheet: -0.40 (0.65), residues: 70
  loop : -0.43 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  60 
 HIS   0.001   0.000   HIS A 140 
 PHE   0.014   0.001   PHE A 702 
 TYR   0.021   0.001   TYR A 483 
 ARG   0.003   0.000   ARG A 900 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.25 seconds
wall clock time: 43 minutes 42.56 seconds (2622.56 seconds total)