Starting phenix.real_space_refine
on Wed Feb 12 10:26:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ptx_13642/02_2025/7ptx_13642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ptx_13642/02_2025/7ptx_13642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2025/7ptx_13642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2025/7ptx_13642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2025/7ptx_13642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2025/7ptx_13642.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    4829      2.51       5
     N    1334      2.21       5
     O    1467      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7653
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1000, 7653
          Classifications: {'peptide': 1000}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 31, 'TRANS': 968}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 306
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 156
  Time building chain proxies: 5.19, per 1000 atoms: 0.68
  Number of scatterers: 7653
  At special positions: 0
  Unit cell: (123.3, 127.8, 90, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1467      8.00
     N    1334      7.00
     C    4829      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.82
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      64.2% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 57
      removed outlier: 3.585A  pdb=" N   VAL A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 62
      removed outlier: 4.185A  pdb=" N   GLY A  61 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 58 through 62'
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 3.708A  pdb=" N   ALA A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
    Processing helix  chain 'A' and resid 90 through 109
    Processing helix  chain 'A' and resid 119 through 147
      removed outlier: 4.018A  pdb=" N   GLU A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU A 142 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLY A 143 " --> pdb=" O   GLU A 139 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   HIS A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 147 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 151
      removed outlier: 3.506A  pdb=" N   ILE A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 151'
    Processing helix  chain 'A' and resid 157 through 178
      removed outlier: 3.739A  pdb=" N   GLU A 175 " --> pdb=" O   ASN A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 190
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 4.502A  pdb=" N   SER A 204 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 3.821A  pdb=" N   LEU A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   SER A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LEU A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA A 225 " --> pdb=" O   ASN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 269
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 3.750A  pdb=" N   ARG A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 348
      removed outlier: 3.763A  pdb=" N   ASN A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LYS A 335 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   THR A 348 " --> pdb=" O   ARG A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 468
    Processing helix  chain 'A' and resid 470 through 484
      removed outlier: 4.159A  pdb=" N   GLY A 476 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 506
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 517 through 524
      removed outlier: 3.544A  pdb=" N   LEU A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN A 523 " --> pdb=" O   ASN A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 541 through 550
      removed outlier: 3.878A  pdb=" N   GLU A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.686A  pdb=" N   ALA A 571 " --> pdb=" O   LEU A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 584
    Processing helix  chain 'A' and resid 601 through 608
      removed outlier: 3.975A  pdb=" N   ILE A 605 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   THR A 606 " --> pdb=" O   LEU A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 618
      removed outlier: 4.369A  pdb=" N   ARG A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASN A 617 " --> pdb=" O   ARG A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 640
    Processing helix  chain 'A' and resid 642 through 653
      removed outlier: 4.250A  pdb=" N   ASN A 653 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 676
    Processing helix  chain 'A' and resid 677 through 687
    Processing helix  chain 'A' and resid 702 through 710
    Processing helix  chain 'A' and resid 713 through 723
      removed outlier: 4.051A  pdb=" N   ARG A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 735
      removed outlier: 4.400A  pdb=" N   ALA A 734 " --> pdb=" O   ARG A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 745
      removed outlier: 3.884A  pdb=" N   LEU A 740 " --> pdb=" O   THR A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 756
    Processing helix  chain 'A' and resid 769 through 777
      removed outlier: 3.883A  pdb=" N   LEU A 773 " --> pdb=" O   THR A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 789
      removed outlier: 4.254A  pdb=" N   GLN A 784 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 811
      removed outlier: 4.173A  pdb=" N   PHE A 806 " --> pdb=" O   THR A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 835 through 844
      removed outlier: 3.840A  pdb=" N   GLU A 839 " --> pdb=" O   MET A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 857
      removed outlier: 4.094A  pdb=" N   VAL A 849 " --> pdb=" O   HIS A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 861
    Processing helix  chain 'A' and resid 870 through 878
    Processing helix  chain 'A' and resid 879 through 889
    Processing helix  chain 'A' and resid 893 through 897
      removed outlier: 3.582A  pdb=" N   ASN A 897 " --> pdb=" O   ASN A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 908
      removed outlier: 3.753A  pdb=" N   SER A 908 " --> pdb=" O   LEU A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 911
      No H-bonds generated for 'chain 'A' and resid 909 through 911'
    Processing helix  chain 'A' and resid 914 through 921
    Processing helix  chain 'A' and resid 935 through 943
      removed outlier: 3.695A  pdb=" N   PHE A 943 " --> pdb=" O   LEU A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 955
      removed outlier: 4.015A  pdb=" N   VAL A 949 " --> pdb=" O   HIS A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 980
      removed outlier: 3.741A  pdb=" N   CYS A 975 " --> pdb=" O   TYR A 971 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ASP A 976 " --> pdb=" O   HIS A 972 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A 977 " --> pdb=" O   ALA A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 999 through 1007
      removed outlier: 3.738A  pdb=" N   GLU A1003 " --> pdb=" O   SER A 999 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR A1007 " --> pdb=" O   GLU A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1021
    Processing helix  chain 'A' and resid 1034 through 1042
    Processing helix  chain 'A' and resid 1054 through 1065
      removed outlier: 3.920A  pdb=" N   VAL A1059 " --> pdb=" O   GLU A1055 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   VAL A1060 " --> pdb=" O   ARG A1056 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU A1061 " --> pdb=" O   LEU A1057 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR A1062 " --> pdb=" O   ASP A1058 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373
    Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 403

    388 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.54

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2577
        1.34 -     1.46: 1185
        1.46 -     1.58: 3976
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 7777
  Sorted by residual:
  bond pdb=" C   ASN A 419 "
       pdb=" N   PRO A 420 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.12e-02 7.97e+03 4.32e+00
  bond pdb=" CB  PRO A 737 "
       pdb=" CG  PRO A 737 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.30e+00
  bond pdb=" C   THR A 782 "
       pdb=" N   PRO A 783 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.46e+00
  bond pdb=" CG  MET A 283 "
       pdb=" SD  MET A 283 "
    ideal  model  delta    sigma   weight residual
    1.803  1.778  0.025 2.50e-02 1.60e+03 9.65e-01
  bond pdb=" CG  GLU A 876 "
       pdb=" CD  GLU A 876 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 9.64e-01
  ... (remaining 7772 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 10186
        1.79 -     3.59: 277
        3.59 -     5.38: 50
        5.38 -     7.18: 19
        7.18 -     8.97: 5
  Bond angle restraints: 10537
  Sorted by residual:
  angle pdb=" CA  PRO A 737 "
        pdb=" N   PRO A 737 "
        pdb=" CD  PRO A 737 "
      ideal   model   delta    sigma   weight residual
     112.00  106.07    5.93 1.40e+00 5.10e-01 1.79e+01
  angle pdb=" N   VAL A  65 "
        pdb=" CA  VAL A  65 "
        pdb=" C   VAL A  65 "
      ideal   model   delta    sigma   weight residual
     112.80  108.59    4.21 1.15e+00 7.56e-01 1.34e+01
  angle pdb=" C   ILE A 832 "
        pdb=" N   ASN A 833 "
        pdb=" CA  ASN A 833 "
      ideal   model   delta    sigma   weight residual
     122.46  127.43   -4.97 1.41e+00 5.03e-01 1.24e+01
  angle pdb=" C   HIS A 282 "
        pdb=" N   MET A 283 "
        pdb=" CA  MET A 283 "
      ideal   model   delta    sigma   weight residual
     121.14  115.15    5.99 1.75e+00 3.27e-01 1.17e+01
  angle pdb=" N   GLU A 876 "
        pdb=" CA  GLU A 876 "
        pdb=" CB  GLU A 876 "
      ideal   model   delta    sigma   weight residual
     110.39  116.05   -5.66 1.66e+00 3.63e-01 1.16e+01
  ... (remaining 10532 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 4195
       16.46 -    32.91: 441
       32.91 -    49.37: 80
       49.37 -    65.83: 13
       65.83 -    82.28: 7
  Dihedral angle restraints: 4736
    sinusoidal: 1814
      harmonic: 2922
  Sorted by residual:
  dihedral pdb=" CA  LYS A 934 "
           pdb=" C   LYS A 934 "
           pdb=" N   SER A 935 "
           pdb=" CA  SER A 935 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.28  -22.72     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  LYS A 699 "
           pdb=" C   LYS A 699 "
           pdb=" N   ASN A 700 "
           pdb=" CA  ASN A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.60   22.40     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  THR A 992 "
           pdb=" C   THR A 992 "
           pdb=" N   LEU A 993 "
           pdb=" CA  LEU A 993 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.02  -21.98     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 4733 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 719
       0.034 -    0.068: 353
       0.068 -    0.102: 105
       0.102 -    0.135: 36
       0.135 -    0.169: 11
  Chirality restraints: 1224
  Sorted by residual:
  chirality pdb=" CA  GLU A 134 "
            pdb=" N   GLU A 134 "
            pdb=" C   GLU A 134 "
            pdb=" CB  GLU A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  PRO A 737 "
            pdb=" N   PRO A 737 "
            pdb=" C   PRO A 737 "
            pdb=" CB  PRO A 737 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.44e-01
  chirality pdb=" CB  VAL A  56 "
            pdb=" CA  VAL A  56 "
            pdb=" CG1 VAL A  56 "
            pdb=" CG2 VAL A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 1221 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 736 "   -0.064 5.00e-02 4.00e+02   9.42e-02 1.42e+01
        pdb=" N   PRO A 737 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO A 737 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 737 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 441 "   -0.041 5.00e-02 4.00e+02   6.23e-02 6.20e+00
        pdb=" N   PRO A 442 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 442 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 442 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 632 "   -0.033 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 633 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 633 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 633 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 883
        2.74 -     3.28: 9100
        3.28 -     3.82: 13154
        3.82 -     4.36: 15240
        4.36 -     4.90: 23646
  Nonbonded interactions: 62023
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 367 "
            pdb=" NZ  LYS A 407 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" NH2 ARG A 512 "
            pdb=" O   PHE A 544 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   GLU A 493 "
            pdb=" NZ  LYS A 527 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   ARG A 610 "
            pdb=" OG1 THR A 614 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   ASN A 439 "
            pdb=" NZ  LYS A 441 "
     model   vdw
     2.252 3.120
  ... (remaining 62018 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:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.820
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7777  Z= 0.215
  Angle     :  0.756   8.972  10537  Z= 0.411
  Chirality :  0.045   0.169   1224
  Planarity :  0.005   0.094   1381
  Dihedral  : 14.083  82.282   2838
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.26), residues: 994
  helix: -0.39 (0.21), residues: 575
  sheet: -3.62 (0.77), residues: 35
  loop : -2.46 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 384 
 HIS   0.004   0.001   HIS A 972 
 PHE   0.020   0.001   PHE A 290 
 TYR   0.025   0.002   TYR A 951 
 ARG   0.005   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  666 MET cc_start: 0.7947 (ppp) cc_final: 0.6675 (ppp)
REVERT: A  901 ASN cc_start: 0.8547 (p0) cc_final: 0.8330 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1888
  time to fit residues: 31.3536
Evaluate side-chains
  90 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    0.3980
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.080072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.068485 restraints weight = 42783.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.070085 restraints weight = 28411.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.071241 restraints weight = 20759.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7777  Z= 0.195
  Angle     :  0.659   6.464  10537  Z= 0.350
  Chirality :  0.043   0.153   1224
  Planarity :  0.005   0.059   1381
  Dihedral  :  5.492  21.941   1058
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.19 %
    Favored  : 91.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.26), residues: 994
  helix: -0.20 (0.21), residues: 590
  sheet: -3.45 (0.74), residues: 35
  loop : -2.45 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 384 
 HIS   0.008   0.001   HIS A 459 
 PHE   0.017   0.001   PHE A 290 
 TYR   0.022   0.002   TYR A 872 
 ARG   0.007   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.7654 (tpt) cc_final: 0.7039 (tpp)
REVERT: A   95 ASP cc_start: 0.8419 (t0) cc_final: 0.8207 (t0)
REVERT: A  127 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8242 (pp20)
REVERT: A  283 MET cc_start: 0.9199 (pmm) cc_final: 0.8692 (pmm)
REVERT: A  666 MET cc_start: 0.8271 (ppp) cc_final: 0.7578 (ppp)
REVERT: A  805 HIS cc_start: 0.7521 (m90) cc_final: 0.7262 (m90)
REVERT: A 1009 HIS cc_start: 0.8221 (m90) cc_final: 0.7980 (m90)
REVERT: A 1011 ASP cc_start: 0.9028 (p0) cc_final: 0.8513 (p0)
REVERT: A 1012 LEU cc_start: 0.9349 (mm) cc_final: 0.9066 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1835
  time to fit residues: 32.1302
Evaluate side-chains
  92 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0870
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 897 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.080335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.068627 restraints weight = 43178.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.070250 restraints weight = 28630.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.071408 restraints weight = 20826.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7777  Z= 0.192
  Angle     :  0.656   5.981  10537  Z= 0.349
  Chirality :  0.044   0.153   1224
  Planarity :  0.005   0.055   1381
  Dihedral  :  5.406  20.698   1058
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.32 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.26), residues: 994
  helix: -0.04 (0.21), residues: 588
  sheet: -3.07 (0.79), residues: 35
  loop : -2.39 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 701 
 HIS   0.005   0.001   HIS A 459 
 PHE   0.018   0.001   PHE A 290 
 TYR   0.016   0.001   TYR A 130 
 ARG   0.007   0.000   ARG A 512 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.7626 (tpt) cc_final: 0.7013 (tpp)
REVERT: A   87 MET cc_start: 0.7943 (ttt) cc_final: 0.7575 (tmm)
REVERT: A   95 ASP cc_start: 0.8472 (t0) cc_final: 0.8252 (t0)
REVERT: A  283 MET cc_start: 0.9076 (pmm) cc_final: 0.8631 (pmm)
REVERT: A  461 ASP cc_start: 0.7617 (m-30) cc_final: 0.7353 (m-30)
REVERT: A  494 MET cc_start: 0.6846 (mpp) cc_final: 0.6596 (mpp)
REVERT: A  666 MET cc_start: 0.8153 (ppp) cc_final: 0.7897 (ppp)
REVERT: A  675 LEU cc_start: 0.8164 (mm) cc_final: 0.7875 (mm)
REVERT: A  776 MET cc_start: 0.8909 (mpp) cc_final: 0.8680 (mpp)
REVERT: A  805 HIS cc_start: 0.7616 (m90) cc_final: 0.7343 (m90)
REVERT: A  851 MET cc_start: 0.8905 (mtm) cc_final: 0.8626 (mtt)
REVERT: A  865 MET cc_start: 0.7784 (tpp) cc_final: 0.7225 (tpp)
REVERT: A 1009 HIS cc_start: 0.8219 (m90) cc_final: 0.7950 (m90)
REVERT: A 1011 ASP cc_start: 0.8978 (p0) cc_final: 0.8619 (p0)
REVERT: A 1012 LEU cc_start: 0.9361 (mm) cc_final: 0.9141 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1769
  time to fit residues: 31.1409
Evaluate side-chains
  95 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0470
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.9684

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.079625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.067877 restraints weight = 43451.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.069460 restraints weight = 28969.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.070593 restraints weight = 21199.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7777  Z= 0.214
  Angle     :  0.666   7.002  10537  Z= 0.353
  Chirality :  0.044   0.155   1224
  Planarity :  0.005   0.056   1381
  Dihedral  :  5.451  20.926   1058
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.59 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.26), residues: 994
  helix:  0.06 (0.21), residues: 580
  sheet: -3.01 (0.82), residues: 35
  loop : -2.32 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 701 
 HIS   0.005   0.001   HIS A 772 
 PHE   0.019   0.002   PHE A 290 
 TYR   0.024   0.002   TYR A1015 
 ARG   0.011   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 ASP cc_start: 0.8384 (t0) cc_final: 0.8162 (t0)
REVERT: A  283 MET cc_start: 0.9238 (pmm) cc_final: 0.8836 (pmm)
REVERT: A  317 LYS cc_start: 0.8783 (pttm) cc_final: 0.8544 (mmmm)
REVERT: A  666 MET cc_start: 0.8212 (ppp) cc_final: 0.7691 (ppp)
REVERT: A  776 MET cc_start: 0.8962 (mpp) cc_final: 0.8718 (mpp)
REVERT: A  805 HIS cc_start: 0.7526 (m90) cc_final: 0.7281 (m90)
REVERT: A  851 MET cc_start: 0.8868 (mtm) cc_final: 0.8570 (mtt)
REVERT: A  901 ASN cc_start: 0.8686 (p0) cc_final: 0.8403 (p0)
REVERT: A 1009 HIS cc_start: 0.8202 (m90) cc_final: 0.7957 (m90)
REVERT: A 1011 ASP cc_start: 0.9091 (p0) cc_final: 0.8620 (p0)
REVERT: A 1012 LEU cc_start: 0.9388 (mm) cc_final: 0.9094 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1992
  time to fit residues: 33.7648
Evaluate side-chains
  90 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0170
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 917 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.080160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.068223 restraints weight = 43075.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.069861 restraints weight = 28364.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.071044 restraints weight = 20635.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7777  Z= 0.193
  Angle     :  0.665   7.696  10537  Z= 0.350
  Chirality :  0.044   0.158   1224
  Planarity :  0.005   0.054   1381
  Dihedral  :  5.345  20.853   1058
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.97 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.26), residues: 994
  helix:  0.06 (0.21), residues: 586
  sheet: -2.76 (0.85), residues: 35
  loop : -2.27 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 384 
 HIS   0.005   0.001   HIS A 772 
 PHE   0.020   0.001   PHE A 290 
 TYR   0.020   0.001   TYR A 130 
 ARG   0.007   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.7198 (ttp) cc_final: 0.6955 (tmm)
REVERT: A   95 ASP cc_start: 0.8460 (t0) cc_final: 0.8214 (t0)
REVERT: A  461 ASP cc_start: 0.7679 (m-30) cc_final: 0.7420 (m-30)
REVERT: A  666 MET cc_start: 0.8199 (ppp) cc_final: 0.7809 (ppp)
REVERT: A  675 LEU cc_start: 0.8138 (mm) cc_final: 0.7608 (mm)
REVERT: A  776 MET cc_start: 0.8851 (mpp) cc_final: 0.8628 (mpp)
REVERT: A  805 HIS cc_start: 0.7574 (m90) cc_final: 0.7269 (m90)
REVERT: A  835 MET cc_start: 0.8166 (mmp) cc_final: 0.7915 (mmp)
REVERT: A  851 MET cc_start: 0.8898 (mtm) cc_final: 0.8583 (mtt)
REVERT: A  852 LEU cc_start: 0.8513 (pp) cc_final: 0.8145 (tt)
REVERT: A  865 MET cc_start: 0.7753 (tpp) cc_final: 0.7186 (tpp)
REVERT: A  901 ASN cc_start: 0.8751 (p0) cc_final: 0.8389 (p0)
REVERT: A 1009 HIS cc_start: 0.8097 (m90) cc_final: 0.7735 (m90)
REVERT: A 1011 ASP cc_start: 0.8973 (p0) cc_final: 0.8454 (p0)
REVERT: A 1012 LEU cc_start: 0.9376 (mm) cc_final: 0.9007 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1816
  time to fit residues: 31.5384
Evaluate side-chains
  96 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 91 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    0.3980
   chunk 36 optimal weight:    5.9990
   chunk 37 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 897 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.080653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.068881 restraints weight = 43538.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.070502 restraints weight = 28714.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.071670 restraints weight = 20926.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7777  Z= 0.191
  Angle     :  0.671   8.097  10537  Z= 0.355
  Chirality :  0.044   0.149   1224
  Planarity :  0.005   0.052   1381
  Dihedral  :  5.293  20.958   1058
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.26), residues: 994
  helix:  0.12 (0.21), residues: 582
  sheet: -2.32 (0.94), residues: 33
  loop : -2.28 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 701 
 HIS   0.004   0.001   HIS A 459 
 PHE   0.017   0.001   PHE A 170 
 TYR   0.022   0.001   TYR A 971 
 ARG   0.005   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASP cc_start: 0.8457 (t0) cc_final: 0.8203 (t0)
REVERT: A  461 ASP cc_start: 0.7768 (m-30) cc_final: 0.7501 (m-30)
REVERT: A  675 LEU cc_start: 0.8173 (mm) cc_final: 0.7595 (mm)
REVERT: A  805 HIS cc_start: 0.7576 (m90) cc_final: 0.7234 (m90)
REVERT: A  835 MET cc_start: 0.8199 (mmp) cc_final: 0.7910 (mmp)
REVERT: A  851 MET cc_start: 0.8860 (mtm) cc_final: 0.8631 (mtt)
REVERT: A  865 MET cc_start: 0.7684 (tpp) cc_final: 0.7107 (tpp)
REVERT: A  918 PHE cc_start: 0.8814 (m-10) cc_final: 0.8552 (m-10)
REVERT: A 1009 HIS cc_start: 0.8144 (m90) cc_final: 0.7797 (m90)
REVERT: A 1011 ASP cc_start: 0.9071 (p0) cc_final: 0.8560 (p0)
REVERT: A 1012 LEU cc_start: 0.9416 (mm) cc_final: 0.9111 (mm)
REVERT: A 1015 TYR cc_start: 0.9019 (m-80) cc_final: 0.8671 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1776
  time to fit residues: 31.7432
Evaluate side-chains
  96 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** 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 = 0.3960 r_free = 0.3960 target = 0.080753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.069008 restraints weight = 43911.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.070634 restraints weight = 29303.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.071793 restraints weight = 21453.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7777  Z= 0.202
  Angle     :  0.694   8.526  10537  Z= 0.360
  Chirality :  0.045   0.166   1224
  Planarity :  0.005   0.053   1381
  Dihedral  :  5.310  20.623   1058
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.26), residues: 994
  helix:  0.10 (0.21), residues: 582
  sheet: -2.11 (0.95), residues: 33
  loop : -2.27 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 701 
 HIS   0.004   0.001   HIS A 905 
 PHE   0.025   0.002   PHE A 918 
 TYR   0.024   0.001   TYR A 130 
 ARG   0.005   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.7255 (ttt) cc_final: 0.6694 (tmm)
REVERT: A   95 ASP cc_start: 0.8480 (t0) cc_final: 0.8218 (t0)
REVERT: A  283 MET cc_start: 0.9083 (pmm) cc_final: 0.8835 (pmm)
REVERT: A  461 ASP cc_start: 0.7737 (m-30) cc_final: 0.7472 (m-30)
REVERT: A  494 MET cc_start: 0.6956 (mpp) cc_final: 0.6754 (mpp)
REVERT: A  805 HIS cc_start: 0.7515 (m90) cc_final: 0.7258 (m90)
REVERT: A  835 MET cc_start: 0.8268 (mmp) cc_final: 0.8020 (mmp)
REVERT: A  851 MET cc_start: 0.8886 (mtm) cc_final: 0.8593 (mtt)
REVERT: A  865 MET cc_start: 0.7676 (tpp) cc_final: 0.7158 (tpp)
REVERT: A 1011 ASP cc_start: 0.8926 (p0) cc_final: 0.8566 (p0)
REVERT: A 1012 LEU cc_start: 0.9338 (mm) cc_final: 0.9089 (mm)
REVERT: A 1015 TYR cc_start: 0.9038 (m-80) cc_final: 0.8687 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2004
  time to fit residues: 33.6674
Evaluate side-chains
  93 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    8.9990
   chunk 39 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0170
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.080907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.069037 restraints weight = 42775.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.070667 restraints weight = 28549.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.071833 restraints weight = 20821.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7777  Z= 0.199
  Angle     :  0.696   8.763  10537  Z= 0.361
  Chirality :  0.045   0.190   1224
  Planarity :  0.005   0.053   1381
  Dihedral  :  5.220  20.823   1058
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.26), residues: 994
  helix:  0.14 (0.21), residues: 583
  sheet: -1.98 (0.96), residues: 33
  loop : -2.20 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 701 
 HIS   0.004   0.001   HIS A 500 
 PHE   0.024   0.002   PHE A 907 
 TYR   0.012   0.001   TYR A 130 
 ARG   0.004   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.7056 (ttt) cc_final: 0.6569 (tmm)
REVERT: A   95 ASP cc_start: 0.8445 (t0) cc_final: 0.8197 (t0)
REVERT: A  283 MET cc_start: 0.9128 (pmm) cc_final: 0.8874 (pmm)
REVERT: A  776 MET cc_start: 0.8769 (mmm) cc_final: 0.8474 (mpp)
REVERT: A  848 ILE cc_start: 0.8942 (mp) cc_final: 0.8713 (mp)
REVERT: A  851 MET cc_start: 0.8822 (mtm) cc_final: 0.8585 (mtt)
REVERT: A  865 MET cc_start: 0.7608 (tpp) cc_final: 0.7099 (tpp)
REVERT: A 1011 ASP cc_start: 0.8920 (p0) cc_final: 0.8336 (p0)
REVERT: A 1012 LEU cc_start: 0.9332 (mm) cc_final: 0.9027 (mm)
REVERT: A 1015 TYR cc_start: 0.8999 (m-80) cc_final: 0.8614 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1696
  time to fit residues: 28.7921
Evaluate side-chains
  92 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 46 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0970
   chunk 75 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.080734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.068622 restraints weight = 43572.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.070308 restraints weight = 28596.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.071526 restraints weight = 20726.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   7777  Z= 0.205
  Angle     :  0.712  10.616  10537  Z= 0.368
  Chirality :  0.045   0.228   1224
  Planarity :  0.005   0.053   1381
  Dihedral  :  5.216  20.850   1058
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.26), residues: 994
  helix:  0.14 (0.21), residues: 583
  sheet: -1.85 (0.97), residues: 33
  loop : -2.17 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 701 
 HIS   0.004   0.001   HIS A 500 
 PHE   0.023   0.002   PHE A 290 
 TYR   0.032   0.002   TYR A 951 
 ARG   0.003   0.000   ARG A 496 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.7149 (ttt) cc_final: 0.6658 (tmm)
REVERT: A   95 ASP cc_start: 0.8470 (t0) cc_final: 0.8219 (t0)
REVERT: A  283 MET cc_start: 0.9126 (pmm) cc_final: 0.8834 (pmm)
REVERT: A  851 MET cc_start: 0.8849 (mtm) cc_final: 0.8584 (mtt)
REVERT: A  852 LEU cc_start: 0.8362 (pp) cc_final: 0.8091 (tp)
REVERT: A  865 MET cc_start: 0.7572 (tpp) cc_final: 0.7086 (tpp)
REVERT: A 1009 HIS cc_start: 0.7882 (m-70) cc_final: 0.7457 (m-70)
REVERT: A 1011 ASP cc_start: 0.9126 (p0) cc_final: 0.8440 (p0)
REVERT: A 1012 LEU cc_start: 0.9396 (mm) cc_final: 0.9029 (mm)
REVERT: A 1015 TYR cc_start: 0.9033 (m-80) cc_final: 0.8667 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1802
  time to fit residues: 29.1269
Evaluate side-chains
  91 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0570
   chunk 91 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 74 optimal weight:    0.1980
   chunk 69 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0980
   overall best weight:    0.3900

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 921 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.081758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.069559 restraints weight = 43168.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.071270 restraints weight = 28443.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.072504 restraints weight = 20607.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   7777  Z= 0.200
  Angle     :  0.720  10.686  10537  Z= 0.368
  Chirality :  0.045   0.234   1224
  Planarity :  0.005   0.053   1381
  Dihedral  :  5.200  21.379   1058
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.37 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.26), residues: 994
  helix:  0.17 (0.21), residues: 584
  sheet: -1.75 (0.97), residues: 35
  loop : -2.14 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 701 
 HIS   0.010   0.001   HIS A 213 
 PHE   0.021   0.002   PHE A 918 
 TYR   0.031   0.002   TYR A 971 
 ARG   0.003   0.000   ARG A 326 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.6936 (ttt) cc_final: 0.6469 (tmm)
REVERT: A   95 ASP cc_start: 0.8465 (t0) cc_final: 0.8195 (t0)
REVERT: A  666 MET cc_start: 0.7899 (ppp) cc_final: 0.7695 (ppp)
REVERT: A  675 LEU cc_start: 0.8118 (mm) cc_final: 0.7741 (mm)
REVERT: A  848 ILE cc_start: 0.8895 (mp) cc_final: 0.8427 (mp)
REVERT: A  865 MET cc_start: 0.7476 (tpp) cc_final: 0.6991 (tpp)
REVERT: A 1009 HIS cc_start: 0.7807 (m-70) cc_final: 0.7329 (m90)
REVERT: A 1011 ASP cc_start: 0.9055 (p0) cc_final: 0.8309 (p0)
REVERT: A 1012 LEU cc_start: 0.9388 (mm) cc_final: 0.9007 (mm)
REVERT: A 1015 TYR cc_start: 0.8989 (m-80) cc_final: 0.8568 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1816
  time to fit residues: 30.9260
Evaluate side-chains
  95 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 72 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 81 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 41 optimal weight:    0.2980
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.081105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.069186 restraints weight = 44206.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.070830 restraints weight = 29449.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.071962 restraints weight = 21566.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   7777  Z= 0.215
  Angle     :  0.724   9.846  10537  Z= 0.374
  Chirality :  0.046   0.232   1224
  Planarity :  0.005   0.052   1381
  Dihedral  :  5.263  21.210   1058
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.26), residues: 994
  helix:  0.13 (0.21), residues: 584
  sheet: -1.75 (0.98), residues: 33
  loop : -2.23 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 701 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.025   0.002   PHE A 290 
 TYR   0.011   0.001   TYR A 262 
 ARG   0.005   0.000   ARG A 613 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2991.21 seconds
wall clock time: 54 minutes 26.74 seconds (3266.74 seconds total)