Starting phenix.real_space_refine
on Sat May 17 09:14:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ier_35391/05_2025/8ier_35391_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ier_35391/05_2025/8ier_35391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ier_35391/05_2025/8ier_35391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ier_35391/05_2025/8ier_35391.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ier_35391/05_2025/8ier_35391_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ier_35391/05_2025/8ier_35391_trim.cif"
  }
  resolution = 4.87
  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=   0.006 sd=   0.060
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
     S      51      5.16       5
     C    4851      2.51       5
     N    1288      2.21       5
     O    1309      1.98       5
     H    7758      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15257
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "P"
      Number of atoms: 15243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 967, 15243
          Classifications: {'peptide': 967}
          Link IDs: {'CIS': 2, 'PTRANS': 62, 'TRANS': 902}
          Chain breaks: 9
    Chain: "P"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'SPM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.71, per 1000 atoms: 0.57
  Number of scatterers: 15257
  At special positions: 0
  Unit cell: (108, 113.4, 116.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      51     16.00
     O    1309      8.00
     N    1288      7.00
     C    4851      6.00
     H    7758      1.00
    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: 4.83
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1804

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      46.0% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.50
  Creating SS restraints...
    Processing helix  chain 'P' and resid 50 through 58
    Processing helix  chain 'P' and resid 58 through 63
      removed outlier: 3.693A  pdb=" N   LEU P  62 " --> pdb=" O   ALA P  58 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU P  63 " --> pdb=" O   GLY P  59 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 58 through 63'
    Processing helix  chain 'P' and resid 64 through 66
      No H-bonds generated for 'chain 'P' and resid 64 through 66'
    Processing helix  chain 'P' and resid 70 through 75
    Processing helix  chain 'P' and resid 195 through 201
    Processing helix  chain 'P' and resid 208 through 215
      removed outlier: 3.548A  pdb=" N   ARG P 212 " --> pdb=" O   ASP P 208 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 227 through 236
    Processing helix  chain 'P' and resid 238 through 253
      removed outlier: 3.731A  pdb=" N   GLN P 244 " --> pdb=" O   TYR P 240 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA P 253 " --> pdb=" O   ALA P 249 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 257 through 286
      removed outlier: 4.244A  pdb=" N   CYS P 262 " --> pdb=" O   TRP P 258 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE P 263 " --> pdb=" O   TYR P 259 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN P 281 " --> pdb=" O   LYS P 277 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER P 282 " --> pdb=" O   THR P 278 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG P 286 " --> pdb=" O   SER P 282 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 402 through 413
      removed outlier: 3.654A  pdb=" N   VAL P 408 " --> pdb=" O   LYS P 404 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 422 through 450
      removed outlier: 3.951A  pdb=" N   ILE P 441 " --> pdb=" O   LEU P 437 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   TYR P 442 " --> pdb=" O   LEU P 438 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 454 through 468
      removed outlier: 3.914A  pdb=" N   ILE P 459 " --> pdb=" O   ASN P 455 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   ARG P 460 " --> pdb=" O   GLU P 456 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA P 461 " --> pdb=" O   ILE P 457 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU P 462 " --> pdb=" O   VAL P 458 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 477 through 490
      removed outlier: 4.035A  pdb=" N   LEU P 482 " --> pdb=" O   THR P 478 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR P 483 " --> pdb=" O   VAL P 479 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 502 through 506
      removed outlier: 4.182A  pdb=" N   LYS P 506 " --> pdb=" O   LEU P 503 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 548 through 557
      removed outlier: 3.724A  pdb=" N   THR P 557 " --> pdb=" O   ARG P 553 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 572 through 582
    Processing helix  chain 'P' and resid 643 through 646
    Processing helix  chain 'P' and resid 656 through 662
      removed outlier: 3.767A  pdb=" N   GLY P 662 " --> pdb=" O   GLU P 658 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 674 through 682
    Processing helix  chain 'P' and resid 731 through 741
      removed outlier: 4.093A  pdb=" N   VAL P 735 " --> pdb=" O   GLN P 731 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 753 through 762
      removed outlier: 3.584A  pdb=" N   THR P 759 " --> pdb=" O   GLN P 755 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   VAL P 760 " --> pdb=" O   THR P 756 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 826 through 834
      removed outlier: 3.532A  pdb=" N   PHE P 830 " --> pdb=" O   SER P 826 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 836 through 840
      removed outlier: 3.612A  pdb=" N   LEU P 840 " --> pdb=" O   PHE P 837 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 841 through 846
      removed outlier: 3.708A  pdb=" N   LEU P 845 " --> pdb=" O   LEU P 841 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   VAL P 846 " --> pdb=" O   PRO P 842 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 841 through 846'
    Processing helix  chain 'P' and resid 855 through 857
      No H-bonds generated for 'chain 'P' and resid 855 through 857'
    Processing helix  chain 'P' and resid 858 through 868
    Processing helix  chain 'P' and resid 882 through 888
    Processing helix  chain 'P' and resid 919 through 951
      removed outlier: 3.758A  pdb=" N   CYS P 925 " --> pdb=" O   ARG P 921 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER P 926 " --> pdb=" O   GLU P 922 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   TYR P 940 " --> pdb=" O   TYR P 936 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   THR P 943 " --> pdb=" O   LEU P 939 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 959 through 962
    Processing helix  chain 'P' and resid 963 through 971
      removed outlier: 3.516A  pdb=" N   ASP P 967 " --> pdb=" O   PHE P 963 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL P 969 " --> pdb=" O   ALA P 965 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 998 through 1022
    Processing helix  chain 'P' and resid 1023 through 1026
    Processing helix  chain 'P' and resid 1046 through 1066
      removed outlier: 3.628A  pdb=" N   SER P1066 " --> pdb=" O   ALA P1062 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1078 through 1098
      removed outlier: 3.517A  pdb=" N   LEU P1095 " --> pdb=" O   VAL P1091 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL P1096 " --> pdb=" O   LEU P1092 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL P1098 " --> pdb=" O   GLY P1094 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1102 through 1107
      removed outlier: 3.779A  pdb=" N   LEU P1106 " --> pdb=" O   LEU P1102 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1112 through 1116
      removed outlier: 3.520A  pdb=" N   PHE P1116 " --> pdb=" O   ASP P1113 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1118 through 1148
      removed outlier: 3.541A  pdb=" N   GLN P1140 " --> pdb=" O   SER P1136 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   CYS P1141 " --> pdb=" O   VAL P1137 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU P1142 " --> pdb=" O   LEU P1138 " (cutoff:3.500A)
      Proline residue:  P1143  - end of helix
    Processing helix  chain 'P' and resid 1156 through 1168
      removed outlier: 3.858A  pdb=" N   LEU P1166 " --> pdb=" O   LEU P1162 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ALA P1167 " --> pdb=" O   GLU P1163 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU P1168 " --> pdb=" O   ARG P1164 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 39 through 41
    Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 105
      removed outlier: 4.415A  pdb=" N   PHE P 103 " --> pdb=" O   LEU P 167 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU P 167 " --> pdb=" O   PHE P 103 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL P 105 " --> pdb=" O   TYR P 165 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   TYR P 165 " --> pdb=" O   VAL P 105 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR P 166 " --> pdb=" O   TYR P 173 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE P 176 " --> pdb=" O   ALA P 181 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ALA P 181 " --> pdb=" O   ILE P 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 294 through 298
    Processing sheet with id=AA4, first strand: chain 'P' and resid 373 through 374
      removed outlier: 3.515A  pdb=" N   ALA P 331 " --> pdb=" O   LEU P 374 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   LEU P 392 " --> pdb=" O   VAL P 334 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 337 through 339
      removed outlier: 3.609A  pdb=" N   GLN P 382 " --> pdb=" O   MET P 339 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'P' and resid 509 through 510
    Processing sheet with id=AA7, first strand: chain 'P' and resid 524 through 525
      removed outlier: 3.692A  pdb=" N   ASP P 524 " --> pdb=" O   ARG P 725 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG P 725 " --> pdb=" O   ASP P 524 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET P 724 " --> pdb=" O   ARG P 686 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG P 686 " --> pdb=" O   MET P 724 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'P' and resid 624 through 627
      removed outlier: 7.307A  pdb=" N   LEU P 690 " --> pdb=" O   LEU P 719 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'P' and resid 772 through 773
      removed outlier: 7.486A  pdb=" N   HIS P 772 " --> pdb=" O   ALA P 824 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'P' and resid 875 through 876
      removed outlier: 6.118A  pdb=" N   MET P 875 " --> pdb=" O   ILE P 893 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    286 hydrogen bonds defined for protein.
    810 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: 8.90

  Time building geometry restraints manager: 5.65 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7732
        1.03 -     1.23: 27
        1.23 -     1.42: 3047
        1.42 -     1.62: 4535
        1.62 -     1.81: 76
  Bond restraints: 15417
  Sorted by residual:
  bond pdb=" N   ARG P  36 "
       pdb=" CA  ARG P  36 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   ARG P  36 "
       pdb=" H   ARG P  36 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" C   PHE P 837 "
       pdb=" N   PRO P 838 "
    ideal  model  delta    sigma   weight residual
    1.334  1.346 -0.012 8.40e-03 1.42e+04 2.04e+00
  bond pdb=" C12 SPM P1201 "
       pdb=" C13 SPM P1201 "
    ideal  model  delta    sigma   weight residual
    1.527  1.502  0.025 2.00e-02 2.50e+03 1.62e+00
  bond pdb=" C2  SPM P1201 "
       pdb=" C3  SPM P1201 "
    ideal  model  delta    sigma   weight residual
    1.527  1.503  0.024 2.00e-02 2.50e+03 1.38e+00
  ... (remaining 15412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 27656
        1.66 -     3.33: 288
        3.33 -     4.99: 37
        4.99 -     6.65: 6
        6.65 -     8.32: 1
  Bond angle restraints: 27988
  Sorted by residual:
  angle pdb=" C   THR P 973 "
        pdb=" N   VAL P 974 "
        pdb=" CA  VAL P 974 "
      ideal   model   delta    sigma   weight residual
     121.70  130.02   -8.32 1.80e+00 3.09e-01 2.13e+01
  angle pdb=" C   HIS P 836 "
        pdb=" N   PHE P 837 "
        pdb=" CA  PHE P 837 "
      ideal   model   delta    sigma   weight residual
     120.09  125.71   -5.62 1.25e+00 6.40e-01 2.02e+01
  angle pdb=" C   LEU P 518 "
        pdb=" N   THR P 519 "
        pdb=" CA  THR P 519 "
      ideal   model   delta    sigma   weight residual
     121.70  126.93   -5.23 1.80e+00 3.09e-01 8.44e+00
  angle pdb=" CB  MET P 875 "
        pdb=" CG  MET P 875 "
        pdb=" SD  MET P 875 "
      ideal   model   delta    sigma   weight residual
     112.70  119.24   -6.54 3.00e+00 1.11e-01 4.75e+00
  angle pdb=" N   ALA P 393 "
        pdb=" CA  ALA P 393 "
        pdb=" C   ALA P 393 "
      ideal   model   delta    sigma   weight residual
     108.24  111.11   -2.87 1.32e+00 5.74e-01 4.71e+00
  ... (remaining 27983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 6580
       17.88 -    35.76: 474
       35.76 -    53.64: 142
       53.64 -    71.51: 37
       71.51 -    89.39: 7
  Dihedral angle restraints: 7240
    sinusoidal: 4025
      harmonic: 3215
  Sorted by residual:
  dihedral pdb=" CA  LYS P 835 "
           pdb=" C   LYS P 835 "
           pdb=" N   HIS P 836 "
           pdb=" CA  HIS P 836 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -134.93  -45.07     0      5.00e+00 4.00e-02 8.12e+01
  dihedral pdb=" CA  ILE P 215 "
           pdb=" C   ILE P 215 "
           pdb=" N   TYR P 216 "
           pdb=" CA  TYR P 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.10  -26.90     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  LEU P 968 "
           pdb=" C   LEU P 968 "
           pdb=" N   VAL P 969 "
           pdb=" CA  VAL P 969 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.71   20.29     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 7237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 782
       0.027 -    0.053: 288
       0.053 -    0.080: 79
       0.080 -    0.106: 66
       0.106 -    0.133: 24
  Chirality restraints: 1239
  Sorted by residual:
  chirality pdb=" CA  VAL P1030 "
            pdb=" N   VAL P1030 "
            pdb=" C   VAL P1030 "
            pdb=" CB  VAL P1030 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE P  90 "
            pdb=" N   ILE P  90 "
            pdb=" C   ILE P  90 "
            pdb=" CB  ILE P  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  chirality pdb=" CA  ILE P1111 "
            pdb=" N   ILE P1111 "
            pdb=" C   ILE P1111 "
            pdb=" CB  ILE P1111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  ... (remaining 1236 not shown)

  Planarity restraints: 2198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR P 940 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        pdb=" C   TYR P 940 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR P 940 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER P 941 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU P 473 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO P 474 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO P 474 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO P 474 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS P  68 "    0.022 5.00e-02 4.00e+02   3.36e-02 1.81e+00
        pdb=" N   PRO P  69 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO P  69 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO P  69 "    0.019 5.00e-02 4.00e+02
  ... (remaining 2195 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 549
        2.16 -     2.77: 28897
        2.77 -     3.38: 39620
        3.38 -     3.99: 46441
        3.99 -     4.60: 71592
  Nonbonded interactions: 187099
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN P 675 "
            pdb=" H   GLN P 675 "
     model   vdw
     1.546 2.450
  nonbonded pdb=" O   THR P 953 "
            pdb=" H   ASN P 955 "
     model   vdw
     1.547 2.450
  nonbonded pdb=" OE1 GLU P 177 "
            pdb=" H   GLU P 177 "
     model   vdw
     1.635 2.450
  nonbonded pdb="HH22 ARG P 201 "
            pdb=" O   ALA P 393 "
     model   vdw
     1.690 2.450
  nonbonded pdb=" O   PRO P1074 "
            pdb=" HG1 THR P1077 "
     model   vdw
     1.701 2.450
  ... (remaining 187094 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:             1.740
  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:             0.240
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     41.380
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4769
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      :  0.002   0.033   7659  Z= 0.097
  Angle     :  0.529   8.316  10416  Z= 0.265
  Chirality :  0.038   0.133   1239
  Planarity :  0.003   0.034   1303
  Dihedral  : 12.911  89.393   2815
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.39 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.30), residues: 947
  helix:  1.69 (0.30), residues: 372
  sheet:  1.03 (0.83), residues: 46
  loop : -2.26 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP P 251 
 HIS   0.002   0.000   HIS P 836 
 PHE   0.008   0.001   PHE P 428 
 TYR   0.016   0.001   TYR P1058 
 ARG   0.004   0.000   ARG P 783 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16280 (  286)
  hydrogen bonds       : angle       5.64702 (  810)
  covalent geometry    : bond        0.00202 ( 7659)
  covalent geometry    : angle       0.52862 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  957 ASN cc_start: 0.7742 (p0) cc_final: 0.7438 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.3574
  time to fit residues: 51.9785
Evaluate side-chains
  86 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 72 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.1980
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0970
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.172716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.158593 restraints weight = 93098.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.163416 restraints weight = 56811.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.165500 restraints weight = 35313.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.4543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4828
moved from start:          0.0609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7659  Z= 0.106
  Angle     :  0.512   5.730  10416  Z= 0.261
  Chirality :  0.038   0.147   1239
  Planarity :  0.003   0.035   1303
  Dihedral  :  3.929  56.212   1057
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.81 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.67 (0.29), residues: 947
  helix:  1.61 (0.30), residues: 374
  sheet:  0.92 (0.82), residues: 46
  loop : -2.28 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP P 306 
 HIS   0.002   0.000   HIS P 190 
 PHE   0.040   0.001   PHE P1132 
 TYR   0.011   0.001   TYR P 216 
 ARG   0.002   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  286)
  hydrogen bonds       : angle       5.10440 (  810)
  covalent geometry    : bond        0.00231 ( 7659)
  covalent geometry    : angle       0.51182 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  231 LEU cc_start: 0.6673 (tp) cc_final: 0.6451 (tp)
REVERT: P  477 MET cc_start: 0.7030 (pmm) cc_final: 0.5941 (mmm)
REVERT: P  957 ASN cc_start: 0.7952 (p0) cc_final: 0.7354 (p0)
REVERT: P 1061 LEU cc_start: 0.7671 (tt) cc_final: 0.7257 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.3410
  time to fit residues: 51.0512
Evaluate side-chains
  84 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 22 optimal weight:    0.1980
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 46 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.167789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.152482 restraints weight = 91724.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.156918 restraints weight = 58156.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.158915 restraints weight = 38116.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5221
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7659  Z= 0.141
  Angle     :  0.566   5.740  10416  Z= 0.291
  Chirality :  0.040   0.158   1239
  Planarity :  0.004   0.037   1303
  Dihedral  :  4.327  49.240   1057
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.87 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.85 (0.29), residues: 947
  helix:  1.47 (0.29), residues: 379
  sheet:  0.61 (0.79), residues: 46
  loop : -2.41 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP P 643 
 HIS   0.003   0.001   HIS P 822 
 PHE   0.023   0.002   PHE P 400 
 TYR   0.019   0.002   TYR P1045 
 ARG   0.002   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  286)
  hydrogen bonds       : angle       4.83313 (  810)
  covalent geometry    : bond        0.00313 ( 7659)
  covalent geometry    : angle       0.56560 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  210 MET cc_start: -0.2985 (tpt) cc_final: -0.4683 (tmm)
REVERT: P  231 LEU cc_start: 0.6986 (tp) cc_final: 0.6748 (tp)
REVERT: P  308 ASP cc_start: 0.8007 (p0) cc_final: 0.7533 (p0)
REVERT: P  477 MET cc_start: 0.6963 (pmm) cc_final: 0.6445 (mmm)
REVERT: P  753 ASN cc_start: 0.7001 (t0) cc_final: 0.6229 (t0)
REVERT: P  875 MET cc_start: 0.8490 (tpp) cc_final: 0.8019 (mmm)
REVERT: P  940 TYR cc_start: 0.7699 (t80) cc_final: 0.7438 (t80)
REVERT: P  957 ASN cc_start: 0.8285 (p0) cc_final: 0.7913 (p0)
REVERT: P 1061 LEU cc_start: 0.7803 (tt) cc_final: 0.7472 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.3698
  time to fit residues: 54.7732
Evaluate side-chains
  84 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
P 101 GLN
** P 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.155827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.138274 restraints weight = 91466.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.141896 restraints weight = 61894.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.144430 restraints weight = 40985.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5914
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   7659  Z= 0.269
  Angle     :  0.823   7.668  10416  Z= 0.436
  Chirality :  0.045   0.209   1239
  Planarity :  0.008   0.189   1303
  Dihedral  :  5.785  47.883   1057
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 18.58
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 11.40 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -2.07 (0.27), residues: 947
  helix:  0.09 (0.27), residues: 384
  sheet: -0.52 (0.63), residues: 65
  loop : -2.83 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP P 643 
 HIS   0.010   0.002   HIS P 772 
 PHE   0.021   0.003   PHE P 945 
 TYR   0.024   0.003   TYR P1045 
 ARG   0.015   0.001   ARG P 762 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04841 (  286)
  hydrogen bonds       : angle       5.48518 (  810)
  covalent geometry    : bond        0.00571 ( 7659)
  covalent geometry    : angle       0.82340 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  103 PHE cc_start: 0.7227 (t80) cc_final: 0.6990 (t80)
REVERT: P  231 LEU cc_start: 0.7442 (tp) cc_final: 0.7187 (tp)
REVERT: P  277 LYS cc_start: 0.5678 (mttt) cc_final: 0.5025 (mmtp)
REVERT: P  477 MET cc_start: 0.7899 (pmm) cc_final: 0.7115 (mtp)
REVERT: P  672 ASP cc_start: 0.8343 (t0) cc_final: 0.8124 (t0)
REVERT: P  736 ILE cc_start: 0.8408 (mm) cc_final: 0.7767 (tp)
REVERT: P  918 MET cc_start: 0.8186 (mmt) cc_final: 0.7986 (mmm)
REVERT: P  940 TYR cc_start: 0.8679 (t80) cc_final: 0.8099 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.3729
  time to fit residues: 55.4932
Evaluate side-chains
  88 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
P 559 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.157502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.139777 restraints weight = 89758.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.144697 restraints weight = 56384.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.146601 restraints weight = 36929.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5838
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7659  Z= 0.150
  Angle     :  0.614   5.563  10416  Z= 0.321
  Chirality :  0.040   0.158   1239
  Planarity :  0.005   0.053   1303
  Dihedral  :  5.111  44.753   1057
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.98 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.81 (0.28), residues: 947
  helix:  0.39 (0.28), residues: 378
  sheet: -0.54 (0.61), residues: 65
  loop : -2.70 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P 251 
 HIS   0.005   0.001   HIS P 190 
 PHE   0.036   0.002   PHE P1132 
 TYR   0.020   0.002   TYR P 216 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  286)
  hydrogen bonds       : angle       5.06107 (  810)
  covalent geometry    : bond        0.00327 ( 7659)
  covalent geometry    : angle       0.61365 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  231 LEU cc_start: 0.7338 (tp) cc_final: 0.7076 (tp)
REVERT: P  277 LYS cc_start: 0.5831 (mttt) cc_final: 0.5308 (mmtp)
REVERT: P  477 MET cc_start: 0.7495 (pmm) cc_final: 0.7062 (mtp)
REVERT: P  736 ILE cc_start: 0.8109 (mm) cc_final: 0.7630 (tp)
REVERT: P  940 TYR cc_start: 0.8527 (t80) cc_final: 0.7784 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.3459
  time to fit residues: 51.4422
Evaluate side-chains
  86 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 88 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.157826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.140779 restraints weight = 90609.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.144659 restraints weight = 61939.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.148059 restraints weight = 40521.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5766
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7659  Z= 0.107
  Angle     :  0.551   5.310  10416  Z= 0.284
  Chirality :  0.040   0.163   1239
  Planarity :  0.004   0.051   1303
  Dihedral  :  4.688  42.577   1057
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.03 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.48 (0.28), residues: 947
  helix:  0.88 (0.28), residues: 375
  sheet: -0.37 (0.61), residues: 65
  loop : -2.68 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P 251 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.024   0.001   PHE P1029 
 TYR   0.017   0.001   TYR P 216 
 ARG   0.005   0.000   ARG P 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03282 (  286)
  hydrogen bonds       : angle       4.72470 (  810)
  covalent geometry    : bond        0.00245 ( 7659)
  covalent geometry    : angle       0.55109 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  210 MET cc_start: -0.2190 (tpt) cc_final: -0.4142 (tmm)
REVERT: P  231 LEU cc_start: 0.7621 (tp) cc_final: 0.7368 (tp)
REVERT: P  477 MET cc_start: 0.7648 (pmm) cc_final: 0.6962 (mtp)
REVERT: P  736 ILE cc_start: 0.8462 (mm) cc_final: 0.7316 (tt)
REVERT: P  940 TYR cc_start: 0.8527 (t80) cc_final: 0.7882 (t80)
REVERT: P 1051 PHE cc_start: 0.6691 (t80) cc_final: 0.6485 (t80)
REVERT: P 1088 LEU cc_start: 0.8087 (tp) cc_final: 0.7643 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3139
  time to fit residues: 46.1901
Evaluate side-chains
  84 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
P 867 GLN
** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.153850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.135449 restraints weight = 87834.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.140007 restraints weight = 56037.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.142002 restraints weight = 37778.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6010
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7659  Z= 0.171
  Angle     :  0.637   6.255  10416  Z= 0.336
  Chirality :  0.040   0.170   1239
  Planarity :  0.005   0.053   1303
  Dihedral  :  5.045  42.911   1057
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.04 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.80 (0.28), residues: 947
  helix:  0.60 (0.28), residues: 379
  sheet: -0.55 (0.60), residues: 65
  loop : -2.89 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P1028 
 HIS   0.012   0.002   HIS P 772 
 PHE   0.030   0.003   PHE P1132 
 TYR   0.016   0.002   TYR P 216 
 ARG   0.005   0.001   ARG P 991 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  286)
  hydrogen bonds       : angle       4.90731 (  810)
  covalent geometry    : bond        0.00365 ( 7659)
  covalent geometry    : angle       0.63724 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  210 MET cc_start: -0.0673 (tpt) cc_final: -0.2586 (tmm)
REVERT: P  231 LEU cc_start: 0.7597 (tp) cc_final: 0.7352 (tp)
REVERT: P  277 LYS cc_start: 0.5888 (mttt) cc_final: 0.5464 (mmtp)
REVERT: P  477 MET cc_start: 0.7800 (pmm) cc_final: 0.7043 (mtp)
REVERT: P  685 TYR cc_start: 0.6919 (m-80) cc_final: 0.6696 (m-10)
REVERT: P  736 ILE cc_start: 0.8655 (mm) cc_final: 0.7586 (tt)
REVERT: P  753 ASN cc_start: 0.7861 (t0) cc_final: 0.6329 (t0)
REVERT: P  940 TYR cc_start: 0.8690 (t80) cc_final: 0.8356 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.3204
  time to fit residues: 50.6369
Evaluate side-chains
  88 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.150568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.131182 restraints weight = 86441.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.135174 restraints weight = 53414.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.138038 restraints weight = 35968.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6111
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7659  Z= 0.174
  Angle     :  0.652   7.474  10416  Z= 0.341
  Chirality :  0.041   0.168   1239
  Planarity :  0.005   0.051   1303
  Dihedral  :  5.210  42.095   1057
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 11.93 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.02 (0.28), residues: 947
  helix:  0.49 (0.28), residues: 371
  sheet: -0.67 (0.58), residues: 65
  loop : -3.03 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP P1028 
 HIS   0.004   0.001   HIS P 372 
 PHE   0.022   0.002   PHE P 963 
 TYR   0.022   0.002   TYR P1045 
 ARG   0.005   0.001   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (  286)
  hydrogen bonds       : angle       4.96953 (  810)
  covalent geometry    : bond        0.00379 ( 7659)
  covalent geometry    : angle       0.65234 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  210 MET cc_start: -0.0049 (tpt) cc_final: -0.1886 (tmm)
REVERT: P  231 LEU cc_start: 0.7594 (tp) cc_final: 0.7356 (tp)
REVERT: P  277 LYS cc_start: 0.6144 (mttt) cc_final: 0.5690 (mmtp)
REVERT: P  477 MET cc_start: 0.7910 (pmm) cc_final: 0.6982 (mtp)
REVERT: P  736 ILE cc_start: 0.8798 (mm) cc_final: 0.7831 (tt)
REVERT: P  748 MET cc_start: 0.6767 (ptp) cc_final: 0.5410 (ptt)
REVERT: P  753 ASN cc_start: 0.8026 (t0) cc_final: 0.6527 (t0)
REVERT: P  940 TYR cc_start: 0.8773 (t80) cc_final: 0.8466 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.3312
  time to fit residues: 46.9246
Evaluate side-chains
  83 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    0.4980
   chunk 86 optimal weight:    3.9990
   chunk 87 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.152583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.133175 restraints weight = 86609.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.137406 restraints weight = 52734.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.140434 restraints weight = 34944.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6010
moved from start:          0.5692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7659  Z= 0.110
  Angle     :  0.557   6.088  10416  Z= 0.286
  Chirality :  0.040   0.152   1239
  Planarity :  0.005   0.047   1303
  Dihedral  :  4.807  40.010   1057
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.30 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.64 (0.28), residues: 947
  helix:  0.88 (0.29), residues: 366
  sheet: -0.49 (0.59), residues: 65
  loop : -2.84 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P 251 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.018   0.001   PHE P1029 
 TYR   0.017   0.001   TYR P1045 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03254 (  286)
  hydrogen bonds       : angle       4.64886 (  810)
  covalent geometry    : bond        0.00243 ( 7659)
  covalent geometry    : angle       0.55665 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  210 MET cc_start: -0.0200 (tpt) cc_final: -0.1928 (tmm)
REVERT: P  231 LEU cc_start: 0.7539 (tp) cc_final: 0.7311 (tp)
REVERT: P  277 LYS cc_start: 0.6066 (mttt) cc_final: 0.5657 (mmtp)
REVERT: P  477 MET cc_start: 0.7732 (pmm) cc_final: 0.6926 (mtp)
REVERT: P  736 ILE cc_start: 0.8682 (mm) cc_final: 0.7644 (tt)
REVERT: P  748 MET cc_start: 0.6635 (ptp) cc_final: 0.5324 (ptt)
REVERT: P  940 TYR cc_start: 0.8679 (t80) cc_final: 0.8395 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.2998
  time to fit residues: 44.2859
Evaluate side-chains
  81 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
P 678 GLN
P 755 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.150076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.130820 restraints weight = 87205.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.135618 restraints weight = 53613.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.137610 restraints weight = 36537.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.6108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7659  Z= 0.159
  Angle     :  0.610   5.733  10416  Z= 0.319
  Chirality :  0.040   0.155   1239
  Planarity :  0.005   0.049   1303
  Dihedral  :  5.007  40.307   1057
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.88 %
    Favored  : 86.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.86 (0.28), residues: 947
  helix:  0.64 (0.28), residues: 375
  sheet: -0.49 (0.58), residues: 64
  loop : -2.99 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP P1028 
 HIS   0.003   0.001   HIS P 372 
 PHE   0.029   0.002   PHE P1128 
 TYR   0.017   0.002   TYR P1045 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  286)
  hydrogen bonds       : angle       4.82853 (  810)
  covalent geometry    : bond        0.00348 ( 7659)
  covalent geometry    : angle       0.60983 (10416)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  101 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8078 (tm-30)
REVERT: P  210 MET cc_start: -0.0112 (tpt) cc_final: -0.1909 (tmm)
REVERT: P  231 LEU cc_start: 0.7604 (tp) cc_final: 0.7394 (tp)
REVERT: P  241 TYR cc_start: 0.5930 (t80) cc_final: 0.5562 (t80)
REVERT: P  244 GLN cc_start: 0.8626 (mm110) cc_final: 0.8332 (mm-40)
REVERT: P  277 LYS cc_start: 0.6268 (mttt) cc_final: 0.5809 (mmtp)
REVERT: P  477 MET cc_start: 0.7785 (pmm) cc_final: 0.7134 (mtp)
REVERT: P  736 ILE cc_start: 0.8753 (mm) cc_final: 0.7754 (tt)
REVERT: P  753 ASN cc_start: 0.8041 (t0) cc_final: 0.7465 (t0)
REVERT: P  940 TYR cc_start: 0.8736 (t80) cc_final: 0.8454 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3401
  time to fit residues: 50.1958
Evaluate side-chains
  90 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
P 281 GLN
** P 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.151517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.131856 restraints weight = 86252.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.137104 restraints weight = 52914.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.139241 restraints weight = 35476.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          0.6142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7659  Z= 0.107
  Angle     :  0.552   5.746  10416  Z= 0.282
  Chirality :  0.039   0.150   1239
  Planarity :  0.005   0.046   1303
  Dihedral  :  4.722  38.837   1057
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.72 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.59 (0.28), residues: 947
  helix:  0.93 (0.28), residues: 370
  sheet: -0.46 (0.58), residues: 65
  loop : -2.84 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP P 643 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.017   0.001   PHE P 906 
 TYR   0.016   0.001   TYR P1058 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  286)
  hydrogen bonds       : angle       4.58016 (  810)
  covalent geometry    : bond        0.00243 ( 7659)
  covalent geometry    : angle       0.55205 (10416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4151.90 seconds
wall clock time: 72 minutes 35.83 seconds (4355.83 seconds total)