Starting phenix.real_space_refine
on Fri Jun 13 22:55:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ier_35391/06_2025/8ier_35391_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ier_35391/06_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_35391/06_2025/8ier_35391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ier_35391/06_2025/8ier_35391.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ier_35391/06_2025/8ier_35391_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ier_35391/06_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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.18, per 1000 atoms: 0.54
  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: 4.02
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.40
  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: 5.60

  Time building geometry restraints manager: 5.00 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:             2.020
  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:             0.280
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     36.650
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.890
-------------------------------------------------------------------------------
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  : 1.125 
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: 0.3624
  time to fit residues: 52.6353
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  : 1.273 
-------------------------------------------------------------------------------
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 = 0.172722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.158606 restraints weight = 93101.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.163424 restraints weight = 56759.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.165498 restraints weight = 35315.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4828
moved from start:          0.0607

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= 0.105
  Angle     :  0.512   5.724  10416  Z= 0.261
  Chirality :  0.038   0.147   1239
  Planarity :  0.003   0.035   1303
  Dihedral  :  3.930  56.264   1057
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.71 %
    Favored  : 92.08 %
  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:  1.62 (0.30), residues: 374
  sheet:  0.92 (0.82), residues: 46
  loop : -2.29 (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        0.04386 (  286)
  hydrogen bonds       : angle       5.10647 (  810)
  covalent geometry    : bond        0.00230 ( 7659)
  covalent geometry    : angle       0.51191 (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  : 1.308 
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: 0.6667 (tp) cc_final: 0.6446 (tp)
REVERT: P  477 MET cc_start: 0.7034 (pmm) cc_final: 0.5942 (mmm)
REVERT: P  957 ASN cc_start: 0.7950 (p0) cc_final: 0.7352 (p0)
REVERT: P 1061 LEU cc_start: 0.7663 (tt) cc_final: 0.7247 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.3752
  time to fit residues: 56.1972
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  : 1.309 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 89 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 46 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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
P1047 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.158424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.141986 restraints weight = 90962.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.145638 restraints weight = 59948.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.149539 restraints weight = 37764.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5729
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.092   7659  Z= 0.289
  Angle     :  0.827   9.217  10416  Z= 0.444
  Chirality :  0.046   0.189   1239
  Planarity :  0.006   0.052   1303
  Dihedral  :  5.833  49.775   1057
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.30 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.64 %
    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: -1.93 (0.27), residues: 947
  helix:  0.22 (0.27), residues: 385
  sheet: -0.16 (0.60), residues: 65
  loop : -2.81 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP P 643 
 HIS   0.005   0.001   HIS P 190 
 PHE   0.086   0.004   PHE P 400 
 TYR   0.038   0.003   TYR P1045 
 ARG   0.005   0.001   ARG P 686 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05157 (  286)
  hydrogen bonds       : angle       5.60959 (  810)
  covalent geometry    : bond        0.00588 ( 7659)
  covalent geometry    : angle       0.82650 (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  : 1.468 
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: P  231 LEU cc_start: 0.7323 (tp) cc_final: 0.7054 (tp)
REVERT: P  285 LEU cc_start: 0.5432 (mm) cc_final: 0.5094 (mm)
REVERT: P  293 MET cc_start: -0.3360 (ptt) cc_final: -0.3695 (ptt)
REVERT: P  477 MET cc_start: 0.7670 (pmm) cc_final: 0.7064 (mtp)
REVERT: P  753 ASN cc_start: 0.7861 (t0) cc_final: 0.7027 (t0)
REVERT: P  875 MET cc_start: 0.8860 (tpp) cc_final: 0.8398 (mmm)
REVERT: P  940 TYR cc_start: 0.8505 (t80) cc_final: 0.7806 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.3702
  time to fit residues: 55.3145
Evaluate side-chains
  79 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0980
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.2188

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

Flipped N/Q/H residues before XYZ refinement:
P 244 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.160431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.144291 restraints weight = 89384.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.148523 restraints weight = 54752.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.150375 restraints weight = 36063.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5640
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7659  Z= 0.127
  Angle     :  0.581   5.481  10416  Z= 0.302
  Chirality :  0.039   0.160   1239
  Planarity :  0.005   0.054   1303
  Dihedral  :  4.979  45.786   1057
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.45 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.33 %
    Favored  : 98.55 %
  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: -1.45 (0.28), residues: 947
  helix:  0.71 (0.28), residues: 380
  sheet: -0.18 (0.61), residues: 65
  loop : -2.56 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.006   0.001   HIS P 772 
 PHE   0.024   0.002   PHE P1029 
 TYR   0.017   0.002   TYR P 216 
 ARG   0.005   0.000   ARG P 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03581 (  286)
  hydrogen bonds       : angle       4.99048 (  810)
  covalent geometry    : bond        0.00279 ( 7659)
  covalent geometry    : angle       0.58111 (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
  101 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 1.214 
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: P  231 LEU cc_start: 0.7306 (tp) cc_final: 0.7031 (tp)
REVERT: P  277 LYS cc_start: 0.5694 (mttt) cc_final: 0.5001 (mmtp)
REVERT: P  285 LEU cc_start: 0.5265 (mm) cc_final: 0.5051 (mm)
REVERT: P  477 MET cc_start: 0.7380 (pmm) cc_final: 0.6845 (mtp)
REVERT: P  753 ASN cc_start: 0.7851 (t0) cc_final: 0.7019 (t0)
REVERT: P  940 TYR cc_start: 0.8396 (t80) cc_final: 0.7471 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3531
  time to fit residues: 52.2813
Evaluate side-chains
  80 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0870
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    1.5562

-------------------------------------------------------------------------------
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 = 0.4441 r_free = 0.4441 target = 0.158135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.139201 restraints weight = 89633.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.144296 restraints weight = 57327.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.146517 restraints weight = 37114.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5777
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7659  Z= 0.138
  Angle     :  0.579   5.471  10416  Z= 0.301
  Chirality :  0.040   0.176   1239
  Planarity :  0.005   0.053   1303
  Dihedral  :  4.761  43.986   1057
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.09 %
    Favored  : 88.70 %
  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: -1.42 (0.29), residues: 947
  helix:  0.89 (0.28), residues: 374
  sheet: -0.18 (0.62), residues: 65
  loop : -2.64 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.006   0.001   HIS P 772 
 PHE   0.014   0.002   PHE P 963 
 TYR   0.018   0.002   TYR P 216 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03268 (  286)
  hydrogen bonds       : angle       4.85297 (  810)
  covalent geometry    : bond        0.00303 ( 7659)
  covalent geometry    : angle       0.57921 (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  : 1.225 
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: P  231 LEU cc_start: 0.7542 (tp) cc_final: 0.7313 (tp)
REVERT: P  277 LYS cc_start: 0.5537 (mttt) cc_final: 0.4938 (mmtp)
REVERT: P  285 LEU cc_start: 0.5217 (mm) cc_final: 0.4897 (mm)
REVERT: P  477 MET cc_start: 0.7704 (pmm) cc_final: 0.7045 (mtp)
REVERT: P  736 ILE cc_start: 0.8576 (mm) cc_final: 0.7977 (tp)
REVERT: P  940 TYR cc_start: 0.8498 (t80) cc_final: 0.7865 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.3291
  time to fit residues: 49.7297
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  : 1.288 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4457 r_free = 0.4457 target = 0.158805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.141868 restraints weight = 88416.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.146191 restraints weight = 56150.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.148119 restraints weight = 38080.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5730
moved from start:          0.4169

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= 0.103
  Angle     :  0.542   5.295  10416  Z= 0.277
  Chirality :  0.039   0.145   1239
  Planarity :  0.004   0.049   1303
  Dihedral  :  4.592  42.499   1057
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.24 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  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: -1.25 (0.29), residues: 947
  helix:  1.04 (0.29), residues: 376
  sheet: -0.16 (0.62), residues: 65
  loop : -2.54 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP P 251 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.030   0.002   PHE P1116 
 TYR   0.015   0.001   TYR P 216 
 ARG   0.003   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  286)
  hydrogen bonds       : angle       4.70390 (  810)
  covalent geometry    : bond        0.00235 ( 7659)
  covalent geometry    : angle       0.54177 (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  : 1.211 
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: P  231 LEU cc_start: 0.7545 (tp) cc_final: 0.7278 (tp)
REVERT: P  277 LYS cc_start: 0.6077 (mttt) cc_final: 0.5442 (mmtp)
REVERT: P  285 LEU cc_start: 0.5256 (mm) cc_final: 0.4978 (mm)
REVERT: P  293 MET cc_start: -0.3606 (ptt) cc_final: -0.3923 (ptt)
REVERT: P  477 MET cc_start: 0.7548 (pmm) cc_final: 0.6919 (mtp)
REVERT: P  736 ILE cc_start: 0.8549 (mm) cc_final: 0.7933 (tp)
REVERT: P  875 MET cc_start: 0.8704 (tpp) cc_final: 0.8421 (mmm)
REVERT: P  940 TYR cc_start: 0.8369 (t80) cc_final: 0.7816 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3176
  time to fit residues: 47.0907
Evaluate side-chains
  80 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 31 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   overall best weight:    2.0064

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

Flipped N/Q/H residues before XYZ refinement:
P1047 ASN
** 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 = 0.4364 r_free = 0.4364 target = 0.152557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.133151 restraints weight = 89280.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.138469 restraints weight = 61837.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.140787 restraints weight = 36084.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6019
moved from start:          0.5057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   7659  Z= 0.179
  Angle     :  0.648   5.630  10416  Z= 0.340
  Chirality :  0.041   0.177   1239
  Planarity :  0.005   0.053   1303
  Dihedral  :  5.106  43.278   1057
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.25 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  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: -1.77 (0.28), residues: 947
  helix:  0.62 (0.28), residues: 379
  sheet: -0.51 (0.59), residues: 65
  loop : -2.87 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP P1028 
 HIS   0.005   0.001   HIS P 772 
 PHE   0.023   0.002   PHE P 906 
 TYR   0.018   0.002   TYR P1045 
 ARG   0.006   0.001   ARG P 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03587 (  286)
  hydrogen bonds       : angle       4.91513 (  810)
  covalent geometry    : bond        0.00398 ( 7659)
  covalent geometry    : angle       0.64808 (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
  104 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.178 
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: P  103 PHE cc_start: 0.7343 (t80) cc_final: 0.7063 (t80)
REVERT: P  210 MET cc_start: -0.0312 (tpt) cc_final: -0.2371 (tmm)
REVERT: P  231 LEU cc_start: 0.7654 (tp) cc_final: 0.7406 (tp)
REVERT: P  277 LYS cc_start: 0.6065 (mttt) cc_final: 0.5639 (mmtp)
REVERT: P  285 LEU cc_start: 0.5798 (mm) cc_final: 0.5500 (mm)
REVERT: P  477 MET cc_start: 0.7741 (pmm) cc_final: 0.7108 (mtp)
REVERT: P  736 ILE cc_start: 0.8709 (mm) cc_final: 0.7676 (tt)
REVERT: P  753 ASN cc_start: 0.7863 (t0) cc_final: 0.6407 (t0)
REVERT: P  940 TYR cc_start: 0.8647 (t80) cc_final: 0.8148 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.3180
  time to fit residues: 49.2553
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  : 1.104 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0270
   chunk 58 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.9240

-------------------------------------------------------------------------------
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 = 0.4407 r_free = 0.4407 target = 0.155051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.137542 restraints weight = 87425.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.142430 restraints weight = 55197.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.144146 restraints weight = 36344.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.4255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5922
moved from start:          0.5155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7659  Z= 0.114
  Angle     :  0.566   6.224  10416  Z= 0.290
  Chirality :  0.039   0.152   1239
  Planarity :  0.005   0.048   1303
  Dihedral  :  4.775  41.240   1057
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.30 %
    Favored  : 88.49 %
  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: -1.50 (0.29), residues: 947
  helix:  0.96 (0.29), residues: 368
  sheet: -0.34 (0.59), residues: 65
  loop : -2.74 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P1028 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.020   0.002   PHE P1029 
 TYR   0.014   0.002   TYR P1058 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03140 (  286)
  hydrogen bonds       : angle       4.67164 (  810)
  covalent geometry    : bond        0.00263 ( 7659)
  covalent geometry    : angle       0.56601 (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
  100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.250 
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: -0.0301 (tpt) cc_final: -0.2474 (tmm)
REVERT: P  231 LEU cc_start: 0.7421 (tp) cc_final: 0.7170 (tp)
REVERT: P  277 LYS cc_start: 0.6396 (mttt) cc_final: 0.5950 (mmtp)
REVERT: P  477 MET cc_start: 0.7398 (pmm) cc_final: 0.6862 (mtp)
REVERT: P  736 ILE cc_start: 0.8623 (mm) cc_final: 0.7559 (tt)
REVERT: P  940 TYR cc_start: 0.8510 (t80) cc_final: 0.7995 (t80)
REVERT: P 1088 LEU cc_start: 0.8298 (tp) cc_final: 0.7898 (mm)
REVERT: P 1133 MET cc_start: 0.4303 (ttp) cc_final: 0.2921 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3199
  time to fit residues: 48.0012
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  : 1.315 
-------------------------------------------------------------------------------
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:    0.0010
   chunk 66 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    0.1980
   chunk 86 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.9588

-------------------------------------------------------------------------------
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 = 0.4407 r_free = 0.4407 target = 0.154866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.137195 restraints weight = 88222.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.141698 restraints weight = 55466.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.143540 restraints weight = 36608.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5936
moved from start:          0.5238

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= 0.111
  Angle     :  0.555   5.712  10416  Z= 0.286
  Chirality :  0.039   0.156   1239
  Planarity :  0.004   0.048   1303
  Dihedral  :  4.669  40.301   1057
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.40 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  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: -1.45 (0.29), residues: 947
  helix:  1.04 (0.29), residues: 367
  sheet: -0.22 (0.59), residues: 65
  loop : -2.76 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P 251 
 HIS   0.003   0.001   HIS P 190 
 PHE   0.031   0.002   PHE P1071 
 TYR   0.013   0.001   TYR P1058 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  286)
  hydrogen bonds       : angle       4.57466 (  810)
  covalent geometry    : bond        0.00251 ( 7659)
  covalent geometry    : angle       0.55507 (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  : 1.052 
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: P  210 MET cc_start: -0.0031 (tpt) cc_final: -0.2149 (tmm)
REVERT: P  231 LEU cc_start: 0.7388 (tp) cc_final: 0.7116 (tp)
REVERT: P  277 LYS cc_start: 0.6422 (mttt) cc_final: 0.5926 (mmtp)
REVERT: P  477 MET cc_start: 0.7370 (pmm) cc_final: 0.6844 (mtp)
REVERT: P  736 ILE cc_start: 0.8642 (mm) cc_final: 0.7528 (tt)
REVERT: P  940 TYR cc_start: 0.8499 (t80) cc_final: 0.7837 (t80)
REVERT: P 1088 LEU cc_start: 0.8278 (tp) cc_final: 0.7937 (mm)
REVERT: P 1133 MET cc_start: 0.4407 (ttp) cc_final: 0.3011 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.3279
  time to fit residues: 48.7383
Evaluate side-chains
  79 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.4350 r_free = 0.4350 target = 0.150480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.129528 restraints weight = 83818.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.134250 restraints weight = 50062.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.137529 restraints weight = 32728.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6103
moved from start:          0.5742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7659  Z= 0.151
  Angle     :  0.605   5.712  10416  Z= 0.316
  Chirality :  0.040   0.153   1239
  Planarity :  0.005   0.049   1303
  Dihedral  :  4.972  40.526   1057
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 13.41 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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: -1.77 (0.28), residues: 947
  helix:  0.75 (0.28), residues: 372
  sheet: -0.38 (0.59), residues: 65
  loop : -2.97 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP P 583 
 HIS   0.005   0.001   HIS P 372 
 PHE   0.021   0.002   PHE P 963 
 TYR   0.020   0.002   TYR P 216 
 ARG   0.004   0.001   ARG P 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03324 (  286)
  hydrogen bonds       : angle       4.76204 (  810)
  covalent geometry    : bond        0.00334 ( 7659)
  covalent geometry    : angle       0.60494 (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
  102 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.137 
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: 0.0299 (tpt) cc_final: -0.1718 (tmm)
REVERT: P  231 LEU cc_start: 0.7515 (tp) cc_final: 0.7241 (tp)
REVERT: P  241 TYR cc_start: 0.5693 (t80) cc_final: 0.5389 (t80)
REVERT: P  277 LYS cc_start: 0.6527 (mttt) cc_final: 0.6036 (mmtp)
REVERT: P  477 MET cc_start: 0.7610 (pmm) cc_final: 0.6904 (mtp)
REVERT: P  574 ASP cc_start: 0.8403 (m-30) cc_final: 0.7853 (p0)
REVERT: P  576 LYS cc_start: 0.8492 (tptp) cc_final: 0.8259 (tptp)
REVERT: P  736 ILE cc_start: 0.8707 (mm) cc_final: 0.7723 (tt)
REVERT: P  753 ASN cc_start: 0.8007 (t0) cc_final: 0.6694 (t0)
REVERT: P  940 TYR cc_start: 0.8690 (t80) cc_final: 0.8417 (t80)
REVERT: P 1088 LEU cc_start: 0.8348 (tp) cc_final: 0.8007 (mm)
REVERT: P 1133 MET cc_start: 0.4365 (ttp) cc_final: 0.3240 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.3437
  time to fit residues: 51.0115
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  : 1.120 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 84 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0070
   chunk 83 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0570
   overall best weight:    0.4116

-------------------------------------------------------------------------------
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 = 0.4378 r_free = 0.4378 target = 0.152865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.131482 restraints weight = 82715.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.136644 restraints weight = 47884.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.140162 restraints weight = 30442.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5964
moved from start:          0.5801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7659  Z= 0.099
  Angle     :  0.548   5.874  10416  Z= 0.279
  Chirality :  0.039   0.151   1239
  Planarity :  0.004   0.046   1303
  Dihedral  :  4.648  38.602   1057
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.56 %
    Favored  : 89.23 %
  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: -1.46 (0.29), residues: 947
  helix:  1.08 (0.29), residues: 370
  sheet: -0.23 (0.58), residues: 65
  loop : -2.82 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP P 251 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.015   0.001   PHE P 906 
 TYR   0.017   0.001   TYR P1058 
 ARG   0.004   0.000   ARG P  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02906 (  286)
  hydrogen bonds       : angle       4.48356 (  810)
  covalent geometry    : bond        0.00227 ( 7659)
  covalent geometry    : angle       0.54808 (10416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4584.55 seconds
wall clock time: 80 minutes 9.10 seconds (4809.10 seconds total)