Starting phenix.real_space_refine
on Sat Aug 23 23:51:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ier_35391/08_2025/8ier_35391_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ier_35391/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ier_35391/08_2025/8ier_35391_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ier_35391/08_2025/8ier_35391_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ier_35391/08_2025/8ier_35391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ier_35391/08_2025/8ier_35391.map"
  }
  resolution = 4.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.22, per 1000 atoms: 0.21
  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: 1.37
  Conformation dependent library (CDL) restraints added in 477.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.46
  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: 3.22

  Time building geometry restraints manager: 1.98 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:             1.950
  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:             0.100
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.610
-------------------------------------------------------------------------------
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 : 6.28
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG P 783 
 TYR   0.016   0.001   TYR P1058 
 PHE   0.008   0.001   PHE P 428 
 TRP   0.002   0.000   TRP P 251 
 HIS   0.002   0.000   HIS P 836 

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

*********************** 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  : 0.420 
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  957 ASN cc_start: 0.7742 (p0) cc_final: 0.7441 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1689
  time to fit residues: 24.8736
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  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0470
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    2.6086

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

Flipped N/Q/H residues before XYZ refinement:
P 101 GLN
P1047 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.161739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.143332 restraints weight = 89975.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.147798 restraints weight = 54684.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.150803 restraints weight = 35609.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.152822 restraints weight = 24669.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.154245 restraints weight = 18123.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5486
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   7659  Z= 0.223
  Angle     :  0.744   6.772  10416  Z= 0.391
  Chirality :  0.043   0.178   1239
  Planarity :  0.005   0.046   1303
  Dihedral  :  5.266  50.214   1057
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.35 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.28), residues: 947
  helix:  0.66 (0.27), residues: 389
  sheet: -0.18 (0.62), residues: 65
  loop : -2.61 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P 745 
 TYR   0.031   0.003   TYR P1045 
 PHE   0.016   0.002   PHE P 934 
 TRP   0.010   0.001   TRP P 258 
 HIS   0.006   0.001   HIS P 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 7659)
  covalent geometry    : angle       0.74415 (10416)
  hydrogen bonds       : bond        0.04347 (  286)
  hydrogen bonds       : angle       5.28167 (  810)

*********************** 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
  110 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.420 
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: 0.6988 (tp) cc_final: 0.6727 (tp)
REVERT: P  308 ASP cc_start: 0.8361 (p0) cc_final: 0.7904 (p0)
REVERT: P  477 MET cc_start: 0.7945 (pmm) cc_final: 0.6860 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1784
  time to fit residues: 27.8177
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  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0270
   chunk 91 optimal weight:    0.5980
   chunk 22 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0570
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 = 0.4537 r_free = 0.4537 target = 0.165410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.149587 restraints weight = 91033.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.153859 restraints weight = 59025.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.157659 restraints weight = 35715.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.158652 restraints weight = 22338.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.159913 restraints weight = 16665.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.4465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5273
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7659  Z= 0.096
  Angle     :  0.527   5.353  10416  Z= 0.266
  Chirality :  0.039   0.148   1239
  Planarity :  0.004   0.039   1303
  Dihedral  :  4.471  46.247   1057
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.13 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.29), residues: 947
  helix:  1.32 (0.29), residues: 369
  sheet: -0.09 (0.73), residues: 55
  loop : -2.35 (0.28), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 201 
 TYR   0.012   0.001   TYR P 216 
 PHE   0.008   0.001   PHE P 168 
 TRP   0.013   0.001   TRP P 643 
 HIS   0.003   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7659)
  covalent geometry    : angle       0.52663 (10416)
  hydrogen bonds       : bond        0.03371 (  286)
  hydrogen bonds       : angle       4.71994 (  810)

*********************** 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
  109 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.440 
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: 0.7145 (tp) cc_final: 0.6891 (tp)
REVERT: P  285 LEU cc_start: 0.5060 (mm) cc_final: 0.4852 (mm)
REVERT: P  308 ASP cc_start: 0.8219 (p0) cc_final: 0.7715 (p0)
REVERT: P  394 VAL cc_start: 0.9022 (m) cc_final: 0.8347 (m)
REVERT: P  477 MET cc_start: 0.7143 (pmm) cc_final: 0.6861 (mtp)
REVERT: P  577 MET cc_start: 0.8923 (ttm) cc_final: 0.8711 (ttt)
REVERT: P  675 GLN cc_start: 0.8494 (pm20) cc_final: 0.8260 (pm20)
REVERT: P  957 ASN cc_start: 0.8045 (p0) cc_final: 0.7380 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1652
  time to fit residues: 25.9651
Evaluate side-chains
  87 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
P 867 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.156924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.139592 restraints weight = 90928.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.143690 restraints weight = 59151.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.147502 restraints weight = 37500.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.148665 restraints weight = 25313.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.148925 restraints weight = 17929.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5762
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   7659  Z= 0.224
  Angle     :  0.690   6.439  10416  Z= 0.365
  Chirality :  0.041   0.174   1239
  Planarity :  0.006   0.057   1303
  Dihedral  :  5.232  46.516   1057
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 11.19 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.28), residues: 947
  helix:  0.52 (0.28), residues: 384
  sheet: -0.40 (0.60), residues: 65
  loop : -2.71 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG P 762 
 TYR   0.017   0.002   TYR P 216 
 PHE   0.060   0.003   PHE P1116 
 TRP   0.010   0.001   TRP P 643 
 HIS   0.009   0.001   HIS P 772 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 7659)
  covalent geometry    : angle       0.68993 (10416)
  hydrogen bonds       : bond        0.03924 (  286)
  hydrogen bonds       : angle       5.15646 (  810)

*********************** 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
  100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.343 
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: 0.7323 (tp) cc_final: 0.7083 (tp)
REVERT: P  285 LEU cc_start: 0.5269 (mm) cc_final: 0.4980 (mm)
REVERT: P  477 MET cc_start: 0.7582 (pmm) cc_final: 0.7103 (mtp)
REVERT: P  577 MET cc_start: 0.9133 (ttm) cc_final: 0.8815 (ttt)
REVERT: P  748 MET cc_start: 0.6802 (ptp) cc_final: 0.5195 (ptm)
REVERT: P  753 ASN cc_start: 0.7845 (t0) cc_final: 0.6943 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1272
  time to fit residues: 18.7244
Evaluate side-chains
  85 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.4401 r_free = 0.4401 target = 0.154219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.135459 restraints weight = 89673.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.139729 restraints weight = 54035.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.142635 restraints weight = 35327.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.144575 restraints weight = 24654.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.145906 restraints weight = 18397.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5913
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7659  Z= 0.201
  Angle     :  0.671   6.560  10416  Z= 0.356
  Chirality :  0.041   0.154   1239
  Planarity :  0.005   0.052   1303
  Dihedral  :  5.335  44.708   1057
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.40 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.28), residues: 947
  helix:  0.32 (0.28), residues: 377
  sheet: -0.69 (0.61), residues: 65
  loop : -2.83 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  78 
 TYR   0.023   0.002   TYR P 216 
 PHE   0.027   0.003   PHE P 963 
 TRP   0.009   0.001   TRP P 251 
 HIS   0.005   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7659)
  covalent geometry    : angle       0.67084 (10416)
  hydrogen bonds       : bond        0.03855 (  286)
  hydrogen bonds       : angle       5.15518 (  810)

*********************** 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
  107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.374 
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: P  231 LEU cc_start: 0.7428 (tp) cc_final: 0.7179 (tp)
REVERT: P  277 LYS cc_start: 0.5776 (mttt) cc_final: 0.5265 (mmtp)
REVERT: P  477 MET cc_start: 0.7881 (pmm) cc_final: 0.7061 (mtp)
REVERT: P  736 ILE cc_start: 0.8408 (mm) cc_final: 0.7939 (tp)
REVERT: P  753 ASN cc_start: 0.8271 (t0) cc_final: 0.7269 (t0)
REVERT: P  854 MET cc_start: 0.8558 (tmm) cc_final: 0.7926 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1448
  time to fit residues: 22.4771
Evaluate side-chains
  87 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 27 optimal weight:    0.3980
   chunk 56 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4409 r_free = 0.4409 target = 0.155067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.137553 restraints weight = 87032.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.141415 restraints weight = 53747.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.144123 restraints weight = 35812.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.145944 restraints weight = 25424.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.147191 restraints weight = 19136.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5842
moved from start:          0.4981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7659  Z= 0.128
  Angle     :  0.584   5.665  10416  Z= 0.302
  Chirality :  0.040   0.168   1239
  Planarity :  0.005   0.053   1303
  Dihedral  :  5.020  42.885   1057
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.77 %
    Favored  : 89.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.28), residues: 947
  helix:  0.63 (0.28), residues: 374
  sheet: -0.64 (0.61), residues: 65
  loop : -2.81 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG P 740 
 TYR   0.018   0.002   TYR P 216 
 PHE   0.025   0.002   PHE P1029 
 TRP   0.010   0.001   TRP P 643 
 HIS   0.004   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7659)
  covalent geometry    : angle       0.58395 (10416)
  hydrogen bonds       : bond        0.03375 (  286)
  hydrogen bonds       : angle       4.85684 (  810)

*********************** 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
  103 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.416 
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: -0.0993 (tpt) cc_final: -0.3090 (tmm)
REVERT: P  231 LEU cc_start: 0.7426 (tp) cc_final: 0.7171 (tp)
REVERT: P  277 LYS cc_start: 0.6310 (mttt) cc_final: 0.5851 (mmtp)
REVERT: P  477 MET cc_start: 0.7717 (pmm) cc_final: 0.6882 (mtp)
REVERT: P  577 MET cc_start: 0.9076 (ttm) cc_final: 0.8852 (ttm)
REVERT: P  736 ILE cc_start: 0.8518 (mm) cc_final: 0.7368 (tt)
REVERT: P  753 ASN cc_start: 0.8176 (t0) cc_final: 0.7125 (t0)
REVERT: P 1133 MET cc_start: 0.4232 (ttp) cc_final: 0.2817 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1376
  time to fit residues: 21.3546
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  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** P1103 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 = 0.4366 r_free = 0.4366 target = 0.151582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.132714 restraints weight = 86281.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.136784 restraints weight = 53023.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.139493 restraints weight = 35441.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.141553 restraints weight = 25562.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.142868 restraints weight = 19127.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5996
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7659  Z= 0.163
  Angle     :  0.613   5.233  10416  Z= 0.323
  Chirality :  0.041   0.164   1239
  Planarity :  0.005   0.053   1303
  Dihedral  :  5.142  42.325   1057
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.46 %
    Favored  : 87.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.28), residues: 947
  helix:  0.56 (0.28), residues: 372
  sheet: -0.74 (0.58), residues: 65
  loop : -2.99 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  78 
 TYR   0.018   0.002   TYR P 216 
 PHE   0.022   0.002   PHE P1029 
 TRP   0.010   0.001   TRP P1028 
 HIS   0.005   0.001   HIS P 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7659)
  covalent geometry    : angle       0.61338 (10416)
  hydrogen bonds       : bond        0.03464 (  286)
  hydrogen bonds       : angle       4.95478 (  810)

*********************** 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
  105 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.321 
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: 0.0122 (tpt) cc_final: -0.1894 (tmm)
REVERT: P  231 LEU cc_start: 0.7489 (tp) cc_final: 0.7226 (tp)
REVERT: P  277 LYS cc_start: 0.6373 (mttt) cc_final: 0.5908 (mmtp)
REVERT: P  477 MET cc_start: 0.7930 (pmm) cc_final: 0.7007 (mtp)
REVERT: P  736 ILE cc_start: 0.8692 (mm) cc_final: 0.7592 (tt)
REVERT: P 1133 MET cc_start: 0.4177 (ttp) cc_final: 0.3017 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1454
  time to fit residues: 22.9354
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  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** P 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.146790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.127896 restraints weight = 87917.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.131993 restraints weight = 55610.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.134965 restraints weight = 36095.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.135863 restraints weight = 26271.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.137780 restraints weight = 21190.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6205
moved from start:          0.6486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7659  Z= 0.209
  Angle     :  0.711   6.974  10416  Z= 0.375
  Chirality :  0.042   0.160   1239
  Planarity :  0.006   0.053   1303
  Dihedral  :  5.735  42.955   1057
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 13.62 %
    Favored  : 86.17 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.27), residues: 947
  helix:  0.08 (0.28), residues: 370
  sheet: -0.86 (0.59), residues: 64
  loop : -3.17 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG P 172 
 TYR   0.019   0.003   TYR P 483 
 PHE   0.033   0.003   PHE P 963 
 TRP   0.016   0.002   TRP P1028 
 HIS   0.006   0.002   HIS P 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 7659)
  covalent geometry    : angle       0.71149 (10416)
  hydrogen bonds       : bond        0.03988 (  286)
  hydrogen bonds       : angle       5.33434 (  810)

*********************** 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
  102 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.429 
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: 0.0240 (tpt) cc_final: -0.1787 (tmm)
REVERT: P  231 LEU cc_start: 0.7586 (tp) cc_final: 0.7355 (tp)
REVERT: P  277 LYS cc_start: 0.6458 (mttt) cc_final: 0.5941 (mmtp)
REVERT: P  477 MET cc_start: 0.8110 (pmm) cc_final: 0.7055 (mmm)
REVERT: P  736 ILE cc_start: 0.8816 (mm) cc_final: 0.7823 (tt)
REVERT: P  753 ASN cc_start: 0.8179 (t0) cc_final: 0.7471 (t0)
REVERT: P 1133 MET cc_start: 0.4700 (ttp) cc_final: 0.3777 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1837
  time to fit residues: 26.6320
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  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** P 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 780 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.148314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.125669 restraints weight = 82074.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.130803 restraints weight = 47878.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.134343 restraints weight = 30732.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.136776 restraints weight = 21307.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.138466 restraints weight = 15687.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6098
moved from start:          0.6567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7659  Z= 0.124
  Angle     :  0.589   5.430  10416  Z= 0.305
  Chirality :  0.040   0.149   1239
  Planarity :  0.005   0.052   1303
  Dihedral  :  5.257  40.315   1057
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.72 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.85 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.28), residues: 947
  helix:  0.51 (0.28), residues: 373
  sheet: -0.83 (0.58), residues: 65
  loop : -3.13 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  78 
 TYR   0.018   0.002   TYR P1058 
 PHE   0.018   0.001   PHE P 906 
 TRP   0.011   0.001   TRP P 643 
 HIS   0.005   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7659)
  covalent geometry    : angle       0.58872 (10416)
  hydrogen bonds       : bond        0.03389 (  286)
  hydrogen bonds       : angle       4.93002 (  810)

*********************** 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
  100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.431 
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  210 MET cc_start: 0.0226 (tpt) cc_final: -0.1730 (tmm)
REVERT: P  231 LEU cc_start: 0.7603 (tp) cc_final: 0.7388 (tp)
REVERT: P  277 LYS cc_start: 0.6313 (mttt) cc_final: 0.5800 (mmtp)
REVERT: P  293 MET cc_start: -0.1860 (ptt) cc_final: -0.2296 (ptt)
REVERT: P  477 MET cc_start: 0.8143 (pmm) cc_final: 0.6995 (mmm)
REVERT: P  577 MET cc_start: 0.9160 (ttm) cc_final: 0.8942 (ttm)
REVERT: P  736 ILE cc_start: 0.8748 (mm) cc_final: 0.7752 (tt)
REVERT: P 1133 MET cc_start: 0.4681 (ttp) cc_final: 0.3782 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.1575
  time to fit residues: 23.2853
Evaluate side-chains
  86 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 83 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    0.1980
   chunk 1 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** P 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.150078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.130553 restraints weight = 87773.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.134709 restraints weight = 53761.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.137623 restraints weight = 35825.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.139666 restraints weight = 25554.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.140749 restraints weight = 19218.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6055
moved from start:          0.6558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7659  Z= 0.108
  Angle     :  0.561   6.107  10416  Z= 0.287
  Chirality :  0.040   0.152   1239
  Planarity :  0.005   0.049   1303
  Dihedral  :  4.925  38.650   1057
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.77 %
    Favored  : 89.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.28), residues: 947
  helix:  0.79 (0.29), residues: 374
  sheet: -0.62 (0.57), residues: 65
  loop : -3.06 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  78 
 TYR   0.018   0.001   TYR P1058 
 PHE   0.016   0.001   PHE P 906 
 TRP   0.013   0.001   TRP P 643 
 HIS   0.003   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7659)
  covalent geometry    : angle       0.56091 (10416)
  hydrogen bonds       : bond        0.03129 (  286)
  hydrogen bonds       : angle       4.72348 (  810)

********************** 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
  101 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.343 
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: 0.0126 (tpt) cc_final: -0.1696 (tmm)
REVERT: P  231 LEU cc_start: 0.7542 (tp) cc_final: 0.7318 (tp)
REVERT: P  277 LYS cc_start: 0.6320 (mttt) cc_final: 0.5846 (mmtp)
REVERT: P  477 MET cc_start: 0.8025 (pmm) cc_final: 0.6951 (mmm)
REVERT: P  577 MET cc_start: 0.9137 (ttm) cc_final: 0.8902 (ttm)
REVERT: P  736 ILE cc_start: 0.8718 (mm) cc_final: 0.7704 (tt)
REVERT: P  918 MET cc_start: 0.8394 (mmt) cc_final: 0.8189 (mmm)
REVERT: P 1133 MET cc_start: 0.4548 (ttp) cc_final: 0.3764 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1579
  time to fit residues: 23.7704
Evaluate side-chains
  85 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    0.2980
   chunk 78 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0970
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.4344 r_free = 0.4344 target = 0.151220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.131574 restraints weight = 86756.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.135783 restraints weight = 52717.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.138801 restraints weight = 34961.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.140712 restraints weight = 24796.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.142113 restraints weight = 18813.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6013
moved from start:          0.6531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7659  Z= 0.099
  Angle     :  0.544   5.803  10416  Z= 0.276
  Chirality :  0.039   0.150   1239
  Planarity :  0.005   0.047   1303
  Dihedral  :  4.628  37.595   1057
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.45 %
    Favored  : 89.33 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.29), residues: 947
  helix:  1.08 (0.29), residues: 369
  sheet: -0.40 (0.57), residues: 65
  loop : -2.93 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  78 
 TYR   0.018   0.001   TYR P1058 
 PHE   0.018   0.001   PHE P 428 
 TRP   0.010   0.001   TRP P 643 
 HIS   0.003   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7659)
  covalent geometry    : angle       0.54413 (10416)
  hydrogen bonds       : bond        0.02925 (  286)
  hydrogen bonds       : angle       4.61250 (  810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2460.75 seconds
wall clock time: 42 minutes 39.80 seconds (2559.80 seconds total)