Starting phenix.real_space_refine
on Tue Apr 29 07:12:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n70_24214/04_2025/7n70_24214_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n70_24214/04_2025/7n70_24214.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n70_24214/04_2025/7n70_24214.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n70_24214/04_2025/7n70_24214.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n70_24214/04_2025/7n70_24214_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n70_24214/04_2025/7n70_24214_trim.cif"
  }
  resolution = 2.8
  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=   0.015
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      49      5.16       5
     Be      1      3.05       5
     C    5158      2.51       5
     N    1340      2.21       5
     O    1401      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7953
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1032, 7900
          Classifications: {'peptide': 1032}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 959}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 43
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {' MG': 1, 'BEF': 1, 'LMT': 1, 'Y01': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 10
  Time building chain proxies: 5.66, per 1000 atoms: 0.71
  Number of scatterers: 7953
  At special positions: 0
  Unit cell: (85.634, 102.943, 134.828, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      49     16.00
     Mg      1     11.99
     F       3      9.00
     O    1401      8.00
     N    1340      7.00
     C    5158      6.00
     Be      1      4.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 885.5 milliseconds
  

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 7 sheets defined
      51.6% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 59 through 68
      removed outlier: 3.526A  pdb=" N   LEU A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 77
      removed outlier: 3.941A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 200 through 212
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 233 through 249
      removed outlier: 3.995A  pdb=" N   GLY A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A 238 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 283
      removed outlier: 4.172A  pdb=" N   CYS A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 393 through 396
      removed outlier: 3.843A  pdb=" N   CYS A 396 " --> pdb=" O   THR A 393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 393 through 396'
    Processing helix  chain 'A' and resid 397 through 405
    Processing helix  chain 'A' and resid 417 through 445
      removed outlier: 3.673A  pdb=" N   LYS A 422 " --> pdb=" O   LYS A 418 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE A 423 " --> pdb=" O   HIS A 419 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 458
    Processing helix  chain 'A' and resid 458 through 464
    Processing helix  chain 'A' and resid 467 through 486
    Processing helix  chain 'A' and resid 492 through 502
      removed outlier: 4.098A  pdb=" N   ASN A 497 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 651 through 656
    Processing helix  chain 'A' and resid 667 through 677
    Processing helix  chain 'A' and resid 695 through 700
      removed outlier: 3.593A  pdb=" N   GLN A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 709
      removed outlier: 3.706A  pdb=" N   VAL A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 737
      removed outlier: 3.991A  pdb=" N   VAL A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 760
    Processing helix  chain 'A' and resid 821 through 832
      removed outlier: 3.547A  pdb=" N   LYS A 830 " --> pdb=" O   GLY A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 842
    Processing helix  chain 'A' and resid 850 through 864
    Processing helix  chain 'A' and resid 874 through 876
      No H-bonds generated for 'chain 'A' and resid 874 through 876'
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 949
      removed outlier: 3.533A  pdb=" N   MET A 913 " --> pdb=" O   GLU A 909 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 949 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 964
    Processing helix  chain 'A' and resid 965 through 973
    Processing helix  chain 'A' and resid 974 through 976
      No H-bonds generated for 'chain 'A' and resid 974 through 976'
    Processing helix  chain 'A' and resid 993 through 1019
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.667A  pdb=" N   PHE A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA A1057 " --> pdb=" O   TYR A1053 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A1060 " --> pdb=" O   LEU A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1073 through 1093
    Processing helix  chain 'A' and resid 1108 through 1145
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
    Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 79
      removed outlier: 3.813A  pdb=" N   GLU A  91 " --> pdb=" O   ARG A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.228A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA A 176 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 303
      removed outlier: 4.555A  pdb=" N   CYS A 291 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   CYS A 312 " --> pdb=" O   CYS A 293 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321
      removed outlier: 6.398A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490
      removed outlier: 6.274A  pdb=" N   GLY A 887 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   SER A 903 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   SER A 889 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL A 868 " --> pdb=" O   VAL A 886 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   ILE A 888 " --> pdb=" O   VAL A 868 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   MET A 870 " --> pdb=" O   ILE A 888 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   THR A 844 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   HIS A 767 " --> pdb=" O   HIS A 817 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   ALA A 819 " --> pdb=" O   HIS A 767 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE A 769 " --> pdb=" O   ALA A 819 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 783 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 531
      removed outlier: 7.131A  pdb=" N   GLY A 517 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LEU A 722 " --> pdb=" O   GLY A 517 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL A 718 " --> pdb=" O   MET A 521 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL A 523 " --> pdb=" O   LEU A 716 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU A 716 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   LEU A 714 " --> pdb=" O   PRO A 525 " (cutoff:3.500A)
      removed outlier: 10.420A  pdb=" N   LYS A 527 " --> pdb=" O   SER A 712 " (cutoff:3.500A)
      removed outlier: 13.360A  pdb=" N   SER A 712 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A 715 " --> pdb=" O   LEU A 685 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ARG A 631 " --> pdb=" O   PRO A 624 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   SER A 633 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG A 622 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   VAL A 635 " --> pdb=" O   LEU A 620 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER A 588 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559

    444 hydrogen bonds defined for protein.
    1257 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: 3.18

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2321
        1.33 -     1.46: 1236
        1.46 -     1.58: 4498
        1.58 -     1.70: 4
        1.70 -     1.82: 73
  Bond restraints: 8132
  Sorted by residual:
  bond pdb=" CAV Y01 A1203 "
       pdb=" CBC Y01 A1203 "
    ideal  model  delta    sigma   weight residual
    1.523  1.619 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" CG  PRO A 689 "
       pdb=" CD  PRO A 689 "
    ideal  model  delta    sigma   weight residual
    1.503  1.347  0.156 3.40e-02 8.65e+02 2.10e+01
  bond pdb=" F2  BEF A1201 "
       pdb="BE   BEF A1201 "
    ideal  model  delta    sigma   weight residual
    1.476  1.560 -0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" CAY Y01 A1203 "
       pdb=" OAW Y01 A1203 "
    ideal  model  delta    sigma   weight residual
    1.332  1.412 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" CAM Y01 A1203 "
       pdb=" CAY Y01 A1203 "
    ideal  model  delta    sigma   weight residual
    1.505  1.577 -0.072 2.00e-02 2.50e+03 1.30e+01
  ... (remaining 8127 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 10983
        2.90 -     5.81: 88
        5.81 -     8.71: 18
        8.71 -    11.62: 4
       11.62 -    14.52: 3
  Bond angle restraints: 11096
  Sorted by residual:
  angle pdb=" N   PRO A 689 "
        pdb=" CD  PRO A 689 "
        pdb=" CG  PRO A 689 "
      ideal   model   delta    sigma   weight residual
     103.20   92.24   10.96 1.50e+00 4.44e-01 5.34e+01
  angle pdb=" CA  PRO A 689 "
        pdb=" N   PRO A 689 "
        pdb=" CD  PRO A 689 "
      ideal   model   delta    sigma   weight residual
     112.00  104.44    7.56 1.40e+00 5.10e-01 2.92e+01
  angle pdb=" CAM Y01 A1203 "
        pdb=" CAY Y01 A1203 "
        pdb=" OAW Y01 A1203 "
      ideal   model   delta    sigma   weight residual
     111.19  125.71  -14.52 3.00e+00 1.11e-01 2.34e+01
  angle pdb=" CAZ Y01 A1203 "
        pdb=" CAV Y01 A1203 "
        pdb=" CBC Y01 A1203 "
      ideal   model   delta    sigma   weight residual
     111.19  124.87  -13.68 3.00e+00 1.11e-01 2.08e+01
  angle pdb=" N   TYR A 935 "
        pdb=" CA  TYR A 935 "
        pdb=" C   TYR A 935 "
      ideal   model   delta    sigma   weight residual
     111.11  116.35   -5.24 1.20e+00 6.94e-01 1.90e+01
  ... (remaining 11091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.25: 4415
       15.25 -    30.50: 381
       30.50 -    45.74: 109
       45.74 -    60.99: 25
       60.99 -    76.24: 9
  Dihedral angle restraints: 4939
    sinusoidal: 1957
      harmonic: 2982
  Sorted by residual:
  dihedral pdb=" CA  PHE A 507 "
           pdb=" C   PHE A 507 "
           pdb=" N   ASP A 508 "
           pdb=" CA  ASP A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.91   17.09     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ALA A 551 "
           pdb=" C   ALA A 551 "
           pdb=" N   THR A 552 "
           pdb=" CA  THR A 552 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.34  -16.66     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  MET A 932 "
           pdb=" CG  MET A 932 "
           pdb=" SD  MET A 932 "
           pdb=" CE  MET A 932 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.08   57.92     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1220
       0.079 -    0.159: 105
       0.159 -    0.238: 1
       0.238 -    0.318: 1
       0.318 -    0.397: 3
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CBG Y01 A1203 "
            pdb=" CAQ Y01 A1203 "
            pdb=" CBD Y01 A1203 "
            pdb=" CBI Y01 A1203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.73    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  TYR A 935 "
            pdb=" N   TYR A 935 "
            pdb=" C   TYR A 935 "
            pdb=" CB  TYR A 935 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CBH Y01 A1203 "
            pdb=" CAT Y01 A1203 "
            pdb=" CAZ Y01 A1203 "
            pdb=" CBF Y01 A1203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.53   -0.32 2.00e-01 2.50e+01 2.62e+00
  ... (remaining 1327 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 688 "   -0.066 5.00e-02 4.00e+02   9.54e-02 1.46e+01
        pdb=" N   PRO A 689 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO A 689 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 689 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A1064 "   -0.040 5.00e-02 4.00e+02   6.08e-02 5.92e+00
        pdb=" N   PRO A1065 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A1065 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A1065 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 962 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.15e+00
        pdb=" C   ASP A 962 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASP A 962 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A 963 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 107
        2.67 -     3.23: 7435
        3.23 -     3.78: 12428
        3.78 -     4.34: 17321
        4.34 -     4.90: 29466
  Nonbonded interactions: 66757
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 508 "
            pdb="MG    MG A1202 "
     model   vdw
     2.109 2.170
  nonbonded pdb=" OD2 ASP A 508 "
            pdb=" F1  BEF A1201 "
     model   vdw
     2.135 2.990
  nonbonded pdb=" F1  BEF A1201 "
            pdb="MG    MG A1202 "
     model   vdw
     2.152 2.120
  nonbonded pdb=" O   THR A 510 "
            pdb="MG    MG A1202 "
     model   vdw
     2.165 2.170
  nonbonded pdb=" OG  SER A 633 "
            pdb=" OE2 GLU A 708 "
     model   vdw
     2.175 3.040
  ... (remaining 66752 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 individual isotropic
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:             225.900
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.570
  Find NCS groups from input model:        0.080
  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:11.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  261.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
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      :  0.011   0.890   8133  Z= 1.010
  Angle     :  0.726  14.519  11096  Z= 0.346
  Chirality :  0.046   0.397   1330
  Planarity :  0.005   0.095   1390
  Dihedral  : 13.221  76.240   3013
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 1018
  helix:  1.16 (0.24), residues: 487
  sheet: -1.29 (0.41), residues: 142
  loop : -0.36 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1023 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.031   0.002   PHE A 103 
 TYR   0.021   0.001   TYR A 935 
 ARG   0.006   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14537 (  444)
  hydrogen bonds       : angle       6.33553 ( 1257)
  covalent geometry    : bond        0.00495 ( 8132)
  covalent geometry    : angle       0.72642 (11096)
  Misc. bond           : bond        0.88966 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A   67 TRP cc_start: 0.7759 (t60) cc_final: 0.7444 (t60)
REVERT: A  220 VAL cc_start: 0.8215 (t) cc_final: 0.7906 (p)
REVERT: A  418 LYS cc_start: 0.7901 (ptmt) cc_final: 0.7671 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 1.1948
  time to fit residues: 137.5089
Evaluate side-chains
  66 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 673 GLN
A 721 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.104553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.080860 restraints weight = 14131.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.83
r_work: 0.2916 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8133  Z= 0.152
  Angle     :  0.588   7.369  11096  Z= 0.282
  Chirality :  0.043   0.137   1330
  Planarity :  0.005   0.056   1390
  Dihedral  :  5.189  55.657   1191
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  8.07 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.27), residues: 1018
  helix:  1.39 (0.24), residues: 490
  sheet: -0.75 (0.42), residues: 138
  loop :  0.06 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  71 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.013   0.001   PHE A1154 
 TYR   0.012   0.001   TYR A 161 
 ARG   0.010   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  444)
  hydrogen bonds       : angle       4.88388 ( 1257)
  covalent geometry    : bond        0.00359 ( 8132)
  covalent geometry    : angle       0.58847 (11096)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7611 (p-90) cc_final: 0.7171 (m-90)
REVERT: A   67 TRP cc_start: 0.8442 (t60) cc_final: 0.7901 (t60)
REVERT: A  220 VAL cc_start: 0.8202 (t) cc_final: 0.7901 (p)
REVERT: A  418 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7351 (ptpt)
REVERT: A  849 MET cc_start: 0.9036 (tpt) cc_final: 0.8523 (tpt)
REVERT: A  941 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (mp)
REVERT: A 1096 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7254 (tm)
  outliers start: 18
  outliers final: 9
  residues processed: 76
  average time/residue: 1.0405
  time to fit residues: 85.5500
Evaluate side-chains
  70 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 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 = 0.3417 r_free = 0.3417 target = 0.103589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.081099 restraints weight = 14332.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.70
r_work: 0.2925 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8133  Z= 0.141
  Angle     :  0.552   6.752  11096  Z= 0.264
  Chirality :  0.042   0.134   1330
  Planarity :  0.004   0.037   1390
  Dihedral  :  4.902  52.560   1191
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  :  9.80 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.05 (0.27), residues: 1018
  helix:  1.59 (0.24), residues: 490
  sheet: -0.54 (0.43), residues: 138
  loop :  0.16 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 170 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.012   0.001   PHE A1154 
 TYR   0.012   0.001   TYR A 161 
 ARG   0.007   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03567 (  444)
  hydrogen bonds       : angle       4.59440 ( 1257)
  covalent geometry    : bond        0.00331 ( 8132)
  covalent geometry    : angle       0.55247 (11096)
  Misc. bond           : bond        0.00067 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7608 (p-90) cc_final: 0.7173 (m-10)
REVERT: A   67 TRP cc_start: 0.8416 (t60) cc_final: 0.7870 (t60)
REVERT: A  220 VAL cc_start: 0.8330 (t) cc_final: 0.8057 (p)
REVERT: A  418 LYS cc_start: 0.8222 (ptmt) cc_final: 0.7409 (ptpt)
REVERT: A  632 MET cc_start: 0.7694 (ptm) cc_final: 0.7395 (ptp)
REVERT: A  662 GLU cc_start: 0.9115 (pm20) cc_final: 0.8911 (pm20)
REVERT: A  941 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8052 (mp)
REVERT: A 1096 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7288 (tm)
  outliers start: 20
  outliers final: 7
  residues processed: 81
  average time/residue: 1.0950
  time to fit residues: 96.3711
Evaluate side-chains
  72 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0030
   chunk 96 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.103944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.081546 restraints weight = 14163.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 2.68
r_work: 0.2934 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8133  Z= 0.126
  Angle     :  0.563  10.416  11096  Z= 0.260
  Chirality :  0.042   0.203   1330
  Planarity :  0.004   0.037   1390
  Dihedral  :  4.667  47.455   1191
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.42 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 (0.27), residues: 1018
  helix:  1.72 (0.24), residues: 491
  sheet: -0.40 (0.44), residues: 137
  loop :  0.25 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.004   0.001   HIS A 408 
 PHE   0.011   0.001   PHE A1154 
 TYR   0.011   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (  444)
  hydrogen bonds       : angle       4.40496 ( 1257)
  covalent geometry    : bond        0.00295 ( 8132)
  covalent geometry    : angle       0.56264 (11096)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7621 (p-90) cc_final: 0.7191 (m-10)
REVERT: A   67 TRP cc_start: 0.8444 (t60) cc_final: 0.7915 (t60)
REVERT: A  220 VAL cc_start: 0.8386 (t) cc_final: 0.8138 (p)
REVERT: A  418 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7467 (ptpt)
REVERT: A  673 GLN cc_start: 0.8410 (tp40) cc_final: 0.8028 (tp-100)
REVERT: A  941 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8105 (mp)
REVERT: A 1096 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7369 (tm)
  outliers start: 19
  outliers final: 7
  residues processed: 79
  average time/residue: 1.3282
  time to fit residues: 113.0118
Evaluate side-chains
  74 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:    0.0270
   chunk 77 optimal weight:    0.3980
   chunk 70 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 53 optimal weight:    0.1980
   chunk 79 optimal weight:    0.5980
   chunk 13 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.3038

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 GLN
A 408 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.105487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.083266 restraints weight = 14158.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.69
r_work: 0.2962 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8133  Z= 0.098
  Angle     :  0.523   8.126  11096  Z= 0.246
  Chirality :  0.041   0.146   1330
  Planarity :  0.004   0.036   1390
  Dihedral  :  4.421  41.459   1191
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.34 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.50 (0.27), residues: 1018
  helix:  2.03 (0.24), residues: 480
  sheet: -0.20 (0.43), residues: 137
  loop :  0.27 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A 170 
 HIS   0.004   0.000   HIS A 408 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A1153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03111 (  444)
  hydrogen bonds       : angle       4.20431 ( 1257)
  covalent geometry    : bond        0.00224 ( 8132)
  covalent geometry    : angle       0.52293 (11096)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7625 (p-90) cc_final: 0.7190 (m-10)
REVERT: A   67 TRP cc_start: 0.8447 (t60) cc_final: 0.7815 (t60)
REVERT: A  220 VAL cc_start: 0.8371 (t) cc_final: 0.8113 (p)
REVERT: A  347 VAL cc_start: 0.8636 (t) cc_final: 0.8323 (m)
REVERT: A  418 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7528 (mttp)
REVERT: A  662 GLU cc_start: 0.9076 (pm20) cc_final: 0.8864 (pm20)
REVERT: A  673 GLN cc_start: 0.8401 (tp40) cc_final: 0.8010 (tp-100)
REVERT: A  785 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7957 (pm20)
REVERT: A  834 LYS cc_start: 0.8245 (pmtt) cc_final: 0.7928 (mmtm)
REVERT: A  941 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8065 (mp)
REVERT: A 1096 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7396 (tm)
  outliers start: 19
  outliers final: 7
  residues processed: 87
  average time/residue: 1.3512
  time to fit residues: 126.6355
Evaluate side-chains
  74 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  785 GLU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.103795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.081438 restraints weight = 14225.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.69
r_work: 0.2923 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8133  Z= 0.145
  Angle     :  0.551   8.568  11096  Z= 0.259
  Chirality :  0.042   0.174   1330
  Planarity :  0.004   0.037   1390
  Dihedral  :  4.360  37.870   1191
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.73 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.53 (0.27), residues: 1018
  helix:  1.92 (0.24), residues: 485
  sheet: -0.07 (0.43), residues: 137
  loop :  0.42 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  71 
 HIS   0.004   0.001   HIS A 408 
 PHE   0.011   0.001   PHE A1154 
 TYR   0.014   0.001   TYR A 161 
 ARG   0.003   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  444)
  hydrogen bonds       : angle       4.21289 ( 1257)
  covalent geometry    : bond        0.00343 ( 8132)
  covalent geometry    : angle       0.55105 (11096)
  Misc. bond           : bond        0.00078 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7602 (p-90) cc_final: 0.7170 (m-10)
REVERT: A   67 TRP cc_start: 0.8446 (t60) cc_final: 0.7939 (t60)
REVERT: A  220 VAL cc_start: 0.8449 (t) cc_final: 0.8197 (p)
REVERT: A  418 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7500 (ptpt)
REVERT: A  673 GLN cc_start: 0.8421 (tp40) cc_final: 0.8021 (tp-100)
REVERT: A  785 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7938 (pm20)
REVERT: A  941 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8139 (mp)
REVERT: A 1096 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7419 (tm)
  outliers start: 19
  outliers final: 10
  residues processed: 75
  average time/residue: 1.1082
  time to fit residues: 89.4623
Evaluate side-chains
  76 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  785 GLU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 20 optimal weight:    0.0060
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0980
   chunk 13 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.082773 restraints weight = 14253.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.69
r_work: 0.2953 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8133  Z= 0.104
  Angle     :  0.522   9.032  11096  Z= 0.246
  Chirality :  0.041   0.174   1330
  Planarity :  0.004   0.036   1390
  Dihedral  :  4.169  32.460   1191
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.76 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.69 (0.27), residues: 1018
  helix:  2.11 (0.24), residues: 479
  sheet:  0.06 (0.43), residues: 137
  loop :  0.41 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.004   0.000   HIS A 408 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03097 (  444)
  hydrogen bonds       : angle       4.11497 ( 1257)
  covalent geometry    : bond        0.00243 ( 8132)
  covalent geometry    : angle       0.52219 (11096)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7591 (p-90) cc_final: 0.7158 (m-10)
REVERT: A   67 TRP cc_start: 0.8452 (t60) cc_final: 0.7919 (t60)
REVERT: A  220 VAL cc_start: 0.8428 (t) cc_final: 0.8174 (p)
REVERT: A  418 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7540 (mttp)
REVERT: A  673 GLN cc_start: 0.8400 (tp40) cc_final: 0.8007 (tp-100)
REVERT: A  941 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: A 1096 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7601 (tm)
  outliers start: 16
  outliers final: 8
  residues processed: 76
  average time/residue: 1.2857
  time to fit residues: 104.5971
Evaluate side-chains
  74 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    0.8980
   chunk 101 optimal weight:    0.2980
   chunk 80 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.082415 restraints weight = 14308.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.70
r_work: 0.2947 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8133  Z= 0.113
  Angle     :  0.524   9.668  11096  Z= 0.248
  Chirality :  0.041   0.160   1330
  Planarity :  0.004   0.036   1390
  Dihedral  :  4.071  27.470   1191
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.99 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.78 (0.27), residues: 1018
  helix:  2.13 (0.24), residues: 479
  sheet:  0.21 (0.43), residues: 139
  loop :  0.49 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 100 
 HIS   0.003   0.000   HIS A 408 
 PHE   0.012   0.001   PHE A1123 
 TYR   0.012   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  444)
  hydrogen bonds       : angle       4.09558 ( 1257)
  covalent geometry    : bond        0.00265 ( 8132)
  covalent geometry    : angle       0.52433 (11096)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7593 (p-90) cc_final: 0.7152 (m-10)
REVERT: A   67 TRP cc_start: 0.8458 (t60) cc_final: 0.7929 (t60)
REVERT: A  220 VAL cc_start: 0.8453 (t) cc_final: 0.8199 (p)
REVERT: A  418 LYS cc_start: 0.8369 (ptmt) cc_final: 0.7553 (mttp)
REVERT: A  673 GLN cc_start: 0.8404 (tp40) cc_final: 0.8014 (tp-100)
REVERT: A  834 LYS cc_start: 0.8200 (pmtt) cc_final: 0.7883 (mmtm)
REVERT: A  941 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8098 (mp)
REVERT: A 1096 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7618 (tm)
  outliers start: 17
  outliers final: 10
  residues processed: 77
  average time/residue: 1.0431
  time to fit residues: 87.0566
Evaluate side-chains
  77 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 102 optimal weight:    0.5980
   chunk 81 optimal weight:    0.2980
   chunk 58 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 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 = 0.3424 r_free = 0.3424 target = 0.104254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.081869 restraints weight = 14538.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.76
r_work: 0.2934 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8133  Z= 0.121
  Angle     :  0.530   9.768  11096  Z= 0.251
  Chirality :  0.041   0.151   1330
  Planarity :  0.004   0.036   1390
  Dihedral  :  4.032  23.322   1191
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.11 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.78 (0.27), residues: 1018
  helix:  2.05 (0.24), residues: 484
  sheet:  0.25 (0.43), residues: 139
  loop :  0.57 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 100 
 HIS   0.002   0.000   HIS A 408 
 PHE   0.010   0.001   PHE A1154 
 TYR   0.012   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  444)
  hydrogen bonds       : angle       4.10213 ( 1257)
  covalent geometry    : bond        0.00287 ( 8132)
  covalent geometry    : angle       0.53024 (11096)
  Misc. bond           : bond        0.00065 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7607 (p-90) cc_final: 0.7143 (m-10)
REVERT: A   67 TRP cc_start: 0.8468 (t60) cc_final: 0.7947 (t60)
REVERT: A  220 VAL cc_start: 0.8472 (t) cc_final: 0.8223 (p)
REVERT: A  418 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7551 (mttp)
REVERT: A  673 GLN cc_start: 0.8410 (tp40) cc_final: 0.8027 (tp-100)
REVERT: A  777 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7564 (pp20)
REVERT: A  834 LYS cc_start: 0.8212 (pmtt) cc_final: 0.7896 (mmtm)
REVERT: A  941 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8075 (mp)
REVERT: A 1096 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7613 (tm)
  outliers start: 17
  outliers final: 9
  residues processed: 79
  average time/residue: 1.0902
  time to fit residues: 92.6524
Evaluate side-chains
  77 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  777 GLU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 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 = 0.3413 r_free = 0.3413 target = 0.103489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.081054 restraints weight = 14180.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.72
r_work: 0.2921 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8133  Z= 0.143
  Angle     :  0.550   9.945  11096  Z= 0.258
  Chirality :  0.042   0.164   1330
  Planarity :  0.004   0.036   1390
  Dihedral  :  4.080  20.758   1191
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.46 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 (0.27), residues: 1018
  helix:  2.01 (0.24), residues: 484
  sheet:  0.22 (0.43), residues: 139
  loop :  0.57 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 408 
 PHE   0.011   0.001   PHE A1154 
 TYR   0.013   0.001   TYR A 161 
 ARG   0.005   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03281 (  444)
  hydrogen bonds       : angle       4.15813 ( 1257)
  covalent geometry    : bond        0.00342 ( 8132)
  covalent geometry    : angle       0.55003 (11096)
  Misc. bond           : bond        0.00089 (    1)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   45 TRP cc_start: 0.7612 (p-90) cc_final: 0.7153 (m-10)
REVERT: A   67 TRP cc_start: 0.8470 (t60) cc_final: 0.7946 (t60)
REVERT: A  220 VAL cc_start: 0.8526 (t) cc_final: 0.8279 (p)
REVERT: A  418 LYS cc_start: 0.8361 (ptmt) cc_final: 0.7499 (ptpt)
REVERT: A  673 GLN cc_start: 0.8409 (tp40) cc_final: 0.8016 (tp-100)
REVERT: A  777 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7561 (pp20)
REVERT: A  785 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7778 (pm20)
REVERT: A  834 LYS cc_start: 0.8207 (pmtt) cc_final: 0.7902 (mmtm)
REVERT: A  941 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: A 1096 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7602 (tm)
  outliers start: 17
  outliers final: 10
  residues processed: 74
  average time/residue: 1.1090
  time to fit residues: 88.5046
Evaluate side-chains
  78 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TRP
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  777 GLU
Chi-restraints excluded: chain A residue  785 GLU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1025 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   chunk 75 optimal weight:    0.0270
   chunk 35 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0770
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 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 = 0.3437 r_free = 0.3437 target = 0.105118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.082914 restraints weight = 14417.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.72
r_work: 0.2958 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8133  Z= 0.101
  Angle     :  0.522   9.449  11096  Z= 0.245
  Chirality :  0.041   0.168   1330
  Planarity :  0.004   0.036   1390
  Dihedral  :  3.945  18.097   1191
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.34 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.89 (0.27), residues: 1018
  helix:  2.14 (0.24), residues: 478
  sheet:  0.30 (0.43), residues: 143
  loop :  0.66 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 170 
 HIS   0.003   0.000   HIS A 408 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.005   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  444)
  hydrogen bonds       : angle       4.03952 ( 1257)
  covalent geometry    : bond        0.00236 ( 8132)
  covalent geometry    : angle       0.52159 (11096)
  Misc. bond           : bond        0.00032 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5658.60 seconds
wall clock time: 101 minutes 7.70 seconds (6067.70 seconds total)