Starting phenix.real_space_refine
on Wed Sep 17 20:53:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vx9_43613/09_2025/8vx9_43613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vx9_43613/09_2025/8vx9_43613.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vx9_43613/09_2025/8vx9_43613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vx9_43613/09_2025/8vx9_43613.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vx9_43613/09_2025/8vx9_43613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vx9_43613/09_2025/8vx9_43613.map"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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      39      5.16       5
     C    7076      2.51       5
     N    2004      2.21       5
     O    2125      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11244
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2028
          Classifications: {'peptide': 259}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 251}
    Chain: "B"
      Number of atoms: 9216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1174, 9216
          Classifications: {'peptide': 1174}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1123}
  Time building chain proxies: 3.07, per 1000 atoms: 0.27
  Number of scatterers: 11244
  At special positions: 0
  Unit cell: (93.272, 96.416, 147.768, 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      39     16.00
     O    2125      8.00
     N    2004      7.00
     C    7076      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: 0.88
  Conformation dependent library (CDL) restraints added in 690.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2666

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 7 sheets defined
      57.0% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 6
      removed outlier: 3.887A  pdb=" N   ASP A   6 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3 through 6'
    Processing helix  chain 'A' and resid 29 through 40
      removed outlier: 4.149A  pdb=" N   GLY A  33 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 58
    Processing helix  chain 'A' and resid 60 through 69
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.817A  pdb=" N   GLY A  80 " --> pdb=" O   GLN A  76 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   GLY A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLU A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 158
    Processing helix  chain 'A' and resid 165 through 180
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 198 through 200
      No H-bonds generated for 'chain 'A' and resid 198 through 200'
    Processing helix  chain 'A' and resid 214 through 224
    Processing helix  chain 'A' and resid 240 through 247
    Processing helix  chain 'A' and resid 248 through 259
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 23 through 35
    Processing helix  chain 'B' and resid 50 through 72
    Processing helix  chain 'B' and resid 76 through 95
    Processing helix  chain 'B' and resid 103 through 118
    Processing helix  chain 'B' and resid 120 through 129
    Processing helix  chain 'B' and resid 130 through 132
      No H-bonds generated for 'chain 'B' and resid 130 through 132'
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'B' and resid 151 through 166
    Processing helix  chain 'B' and resid 169 through 182
    Processing helix  chain 'B' and resid 192 through 224
    Processing helix  chain 'B' and resid 225 through 246
      removed outlier: 3.924A  pdb=" N   LEU B 229 " --> pdb=" O   GLU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 267
      removed outlier: 3.566A  pdb=" N   SER B 267 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 285 through 299
    Processing helix  chain 'B' and resid 308 through 310
      No H-bonds generated for 'chain 'B' and resid 308 through 310'
    Processing helix  chain 'B' and resid 311 through 318
    Processing helix  chain 'B' and resid 334 through 349
      removed outlier: 3.876A  pdb=" N   ILE B 338 " --> pdb=" O   GLY B 334 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY B 349 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 375
    Processing helix  chain 'B' and resid 393 through 398
    Processing helix  chain 'B' and resid 407 through 418
    Processing helix  chain 'B' and resid 419 through 423
      removed outlier: 3.688A  pdb=" N   ILE B 422 " --> pdb=" O   PRO B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 454
    Processing helix  chain 'B' and resid 457 through 461
      removed outlier: 3.521A  pdb=" N   ARG B 461 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 485
      removed outlier: 3.631A  pdb=" N   LEU B 476 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE B 479 " --> pdb=" O   GLN B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 568
    Processing helix  chain 'B' and resid 578 through 583
      removed outlier: 3.894A  pdb=" N   VAL B 582 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLU B 583 " --> pdb=" O   ARG B 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 578 through 583'
    Processing helix  chain 'B' and resid 583 through 595
      removed outlier: 4.270A  pdb=" N   GLU B 587 " --> pdb=" O   GLU B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 608
    Processing helix  chain 'B' and resid 609 through 618
      removed outlier: 3.872A  pdb=" N   GLU B 618 " --> pdb=" O   SER B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 631
    Processing helix  chain 'B' and resid 642 through 655
      removed outlier: 3.540A  pdb=" N   ARG B 646 " --> pdb=" O   PRO B 642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 670
    Processing helix  chain 'B' and resid 691 through 701
      removed outlier: 3.540A  pdb=" N   ARG B 701 " --> pdb=" O   ASN B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 720 through 734
    Processing helix  chain 'B' and resid 742 through 760
    Processing helix  chain 'B' and resid 762 through 773
    Processing helix  chain 'B' and resid 786 through 813
    Processing helix  chain 'B' and resid 821 through 830
    Processing helix  chain 'B' and resid 833 through 842
      removed outlier: 3.590A  pdb=" N   ARG B 841 " --> pdb=" O   ARG B 837 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR B 842 " --> pdb=" O   SER B 838 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 844 through 866
      removed outlier: 3.534A  pdb=" N   ARG B 848 " --> pdb=" O   ASP B 844 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 867 through 878
    Processing helix  chain 'B' and resid 881 through 889
    Processing helix  chain 'B' and resid 890 through 904
    Processing helix  chain 'B' and resid 912 through 923
    Processing helix  chain 'B' and resid 938 through 948
      removed outlier: 4.253A  pdb=" N   ILE B 942 " --> pdb=" O   ASP B 938 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 958 through 969
      removed outlier: 3.707A  pdb=" N   GLU B 962 " --> pdb=" O   THR B 958 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE B 966 " --> pdb=" O   GLU B 962 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL B 967 " --> pdb=" O   THR B 963 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 974 through 989
    Processing helix  chain 'B' and resid 1006 through 1011
    Processing helix  chain 'B' and resid 1020 through 1028
      removed outlier: 3.503A  pdb=" N   GLY B1028 " --> pdb=" O   LEU B1024 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1031 through 1043
      removed outlier: 3.645A  pdb=" N   ILE B1036 " --> pdb=" O   ARG B1032 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1048 through 1056
    Processing helix  chain 'B' and resid 1059 through 1065
    Processing helix  chain 'B' and resid 1078 through 1085
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13
      removed outlier: 7.358A  pdb=" N   GLN A  21 " --> pdb=" O   CYS A 235 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ARG A 237 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE A  23 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 125
    Processing sheet with id=AA3, first strand: chain 'B' and resid 381 through 383
      removed outlier: 6.822A  pdb=" N   SER B 382 " --> pdb=" O   VAL B 405 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   ARG B 352 " --> pdb=" O   VAL B 425 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU B 427 " --> pdb=" O   ARG B 352 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 522 through 531
      removed outlier: 4.725A  pdb=" N   ALA B 523 " --> pdb=" O   VAL B 519 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL B 519 " --> pdb=" O   ALA B 523 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TRP B 525 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   LEU B 517 " --> pdb=" O   TRP B 525 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   SER B 527 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   LEU B 515 " --> pdb=" O   SER B 527 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   GLY B 513 " --> pdb=" O   PHE B 529 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B 518 " --> pdb=" O   PHE B 503 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   PHE B 503 " --> pdb=" O   SER B 518 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ARG B 500 " --> pdb=" O   GLY B 711 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   VAL B 713 " --> pdb=" O   ARG B 500 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLN B 502 " --> pdb=" O   VAL B 713 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   TYR B 715 " --> pdb=" O   GLN B 502 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLY B 504 " --> pdb=" O   TYR B 715 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ILE B 717 " --> pdb=" O   GLY B 504 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL B 506 " --> pdb=" O   ILE B 717 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ILE B 678 " --> pdb=" O   ILE B 714 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR B 575 " --> pdb=" O   VAL B 679 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 684 through 685
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1095 through 1096
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1095 through 1096
      removed outlier: 8.150A  pdb=" N   LEU B1150 " --> pdb=" O   LEU B1118 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   LEU B1118 " --> pdb=" O   LEU B1150 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL B1152 " --> pdb=" O   LEU B1116 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   TYR B1119 " --> pdb=" O   HIS B1126 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   HIS B1125 " --> pdb=" O   ILE B1138 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL B1127 " --> pdb=" O   GLY B1136 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY B1136 " --> pdb=" O   VAL B1127 " (cutoff:3.500A)

    607 hydrogen bonds defined for protein.
    1776 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: 2.51

  Time building geometry restraints manager: 1.25 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: 3841
        1.34 -     1.46: 1698
        1.46 -     1.57: 5854
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 11459
  Sorted by residual:
  bond pdb=" C   TRP B1070 "
       pdb=" N   PRO B1071 "
    ideal  model  delta    sigma   weight residual
    1.331  1.349 -0.017 1.20e-02 6.94e+03 2.12e+00
  bond pdb=" C   LEU B 975 "
       pdb=" O   LEU B 975 "
    ideal  model  delta    sigma   weight residual
    1.244  1.229  0.014 1.00e-02 1.00e+04 2.04e+00
  bond pdb=" CG1 ILE B1025 "
       pdb=" CD1 ILE B1025 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.58e+00
  bond pdb=" CA  TYR B 973 "
       pdb=" C   TYR B 973 "
    ideal  model  delta    sigma   weight residual
    1.526  1.510  0.016 1.29e-02 6.01e+03 1.49e+00
  bond pdb=" CA  TRP B 977 "
       pdb=" C   TRP B 977 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.27e-02 6.20e+03 1.39e+00
  ... (remaining 11454 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 15113
        1.65 -     3.30: 352
        3.30 -     4.95: 67
        4.95 -     6.60: 11
        6.60 -     8.25: 3
  Bond angle restraints: 15546
  Sorted by residual:
  angle pdb=" N   TYR B 973 "
        pdb=" CA  TYR B 973 "
        pdb=" C   TYR B 973 "
      ideal   model   delta    sigma   weight residual
     111.54  104.95    6.59 1.36e+00 5.41e-01 2.34e+01
  angle pdb=" CA  LEU B 975 "
        pdb=" C   LEU B 975 "
        pdb=" N   PRO B 976 "
      ideal   model   delta    sigma   weight residual
     120.77  117.27    3.50 9.70e-01 1.06e+00 1.30e+01
  angle pdb=" N   TRP B 977 "
        pdb=" CA  TRP B 977 "
        pdb=" C   TRP B 977 "
      ideal   model   delta    sigma   weight residual
     111.07  107.35    3.72 1.07e+00 8.73e-01 1.21e+01
  angle pdb=" N   PHE B 966 "
        pdb=" CA  PHE B 966 "
        pdb=" C   PHE B 966 "
      ideal   model   delta    sigma   weight residual
     113.20  109.04    4.16 1.21e+00 6.83e-01 1.18e+01
  angle pdb=" N   ASN B 969 "
        pdb=" CA  ASN B 969 "
        pdb=" C   ASN B 969 "
      ideal   model   delta    sigma   weight residual
     114.64  109.90    4.74 1.52e+00 4.33e-01 9.71e+00
  ... (remaining 15541 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 6283
       17.78 -    35.57: 530
       35.57 -    53.35: 76
       53.35 -    71.14: 16
       71.14 -    88.92: 12
  Dihedral angle restraints: 6917
    sinusoidal: 2790
      harmonic: 4127
  Sorted by residual:
  dihedral pdb=" CA  ASP B 324 "
           pdb=" C   ASP B 324 "
           pdb=" N   LEU B 325 "
           pdb=" CA  LEU B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  PHE B 930 "
           pdb=" C   PHE B 930 "
           pdb=" N   ILE B 931 "
           pdb=" CA  ILE B 931 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ARG A 240 "
           pdb=" C   ARG A 240 "
           pdb=" N   HIS A 241 "
           pdb=" CA  HIS A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.10  -16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1068
       0.031 -    0.062: 433
       0.062 -    0.094: 173
       0.094 -    0.125: 71
       0.125 -    0.156: 7
  Chirality restraints: 1752
  Sorted by residual:
  chirality pdb=" CG  LEU B 229 "
            pdb=" CB  LEU B 229 "
            pdb=" CD1 LEU B 229 "
            pdb=" CD2 LEU B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  PRO B 642 "
            pdb=" N   PRO B 642 "
            pdb=" C   PRO B 642 "
            pdb=" CB  PRO B 642 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  VAL B 967 "
            pdb=" N   VAL B 967 "
            pdb=" C   VAL B 967 "
            pdb=" CB  VAL B 967 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1749 not shown)

  Planarity restraints: 2032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 256 "    0.015 2.00e-02 2.50e+03   1.52e-02 4.02e+00
        pdb=" CG  PHE B 256 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 256 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 256 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 256 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 256 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 256 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 375 "   -0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO B 376 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 376 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 376 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 641 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.57e+00
        pdb=" N   PRO B 642 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 642 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 642 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2029 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1768
        2.76 -     3.29: 11710
        3.29 -     3.83: 20141
        3.83 -     4.36: 24122
        4.36 -     4.90: 40029
  Nonbonded interactions: 97770
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B1060 "
            pdb=" NE2 HIS B1064 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   GLY B 389 "
            pdb=" NZ  LYS B 410 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" O   THR A 100 "
            pdb=" NZ  LYS A 103 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OD1 ASP B 591 "
            pdb=" NH1 ARG B 595 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" NZ  LYS A 108 "
            pdb=" OD2 ASP B 200 "
     model   vdw
     2.285 3.120
  ... (remaining 97765 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             3.070
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.090
  Find NCS groups from input model:        0.060
  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:10.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
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      :  0.004   0.049  11459  Z= 0.175
  Angle     :  0.625   8.250  15546  Z= 0.344
  Chirality :  0.042   0.156   1752
  Planarity :  0.005   0.048   2032
  Dihedral  : 13.765  88.924   4251
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.08 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.22), residues: 1429
  helix:  0.62 (0.19), residues: 756
  sheet: -0.90 (0.48), residues: 125
  loop : -1.36 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 175 
 TYR   0.017   0.002   TYR B  58 
 PHE   0.035   0.002   PHE B 256 
 TRP   0.026   0.002   TRP B 563 
 HIS   0.007   0.001   HIS B 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11459)
  covalent geometry    : angle       0.62491 (15546)
  hydrogen bonds       : bond        0.15086 (  605)
  hydrogen bonds       : angle       6.55370 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.1215 (tpp) cc_final: 0.0975 (tpp)
REVERT: A   19 TYR cc_start: 0.7481 (t80) cc_final: 0.6363 (t80)
REVERT: A  125 ILE cc_start: 0.8230 (mt) cc_final: 0.8013 (mt)
REVERT: A  179 GLN cc_start: 0.6997 (mt0) cc_final: 0.6743 (mm-40)
REVERT: B   76 ASP cc_start: 0.6579 (m-30) cc_final: 0.5885 (m-30)
REVERT: B  130 MET cc_start: 0.8339 (mtp) cc_final: 0.8134 (mtm)
REVERT: B  525 TRP cc_start: 0.7554 (p90) cc_final: 0.7340 (p90)
REVERT: B  602 PHE cc_start: 0.8145 (t80) cc_final: 0.7879 (t80)
REVERT: B  715 TYR cc_start: 0.7976 (t80) cc_final: 0.7745 (t80)
REVERT: B  852 LYS cc_start: 0.7142 (tttt) cc_final: 0.6894 (tttt)
REVERT: B  977 TRP cc_start: 0.4842 (t60) cc_final: 0.4571 (t-100)
  outliers start: 1
  outliers final: 2
  residues processed: 259
  average time/residue: 0.6750
  time to fit residues: 188.2144
Evaluate side-chains
  228 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  459 ASP
Chi-restraints excluded: chain B residue  796 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.3980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 ASN
B 178 GLN
B 494 ASN
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.184840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.170397 restraints weight = 15175.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 1.71
r_work: 0.4150 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.4021 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11459  Z= 0.163
  Angle     :  0.628  10.893  15546  Z= 0.321
  Chirality :  0.044   0.168   1752
  Planarity :  0.005   0.063   2032
  Dihedral  :  5.406  86.584   1582
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 10.13 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.22), residues: 1429
  helix:  0.78 (0.19), residues: 762
  sheet: -1.23 (0.43), residues: 144
  loop : -1.29 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1151 
 TYR   0.020   0.002   TYR B 874 
 PHE   0.022   0.002   PHE B1046 
 TRP   0.013   0.002   TRP B 977 
 HIS   0.006   0.001   HIS B 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (11459)
  covalent geometry    : angle       0.62803 (15546)
  hydrogen bonds       : bond        0.04485 (  605)
  hydrogen bonds       : angle       5.16941 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 229
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.1245 (tpp) cc_final: 0.1002 (tpp)
REVERT: A  140 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7714 (mmmt)
REVERT: A  179 GLN cc_start: 0.7216 (mt0) cc_final: 0.6945 (mm-40)
REVERT: B   35 TRP cc_start: 0.7244 (OUTLIER) cc_final: 0.6626 (m-10)
REVERT: B  162 PHE cc_start: 0.6934 (t80) cc_final: 0.6521 (t80)
REVERT: B  321 ASP cc_start: 0.7264 (p0) cc_final: 0.7046 (p0)
REVERT: B  525 TRP cc_start: 0.7486 (p90) cc_final: 0.7248 (p90)
REVERT: B  602 PHE cc_start: 0.8175 (t80) cc_final: 0.7912 (t80)
REVERT: B  615 LEU cc_start: 0.6613 (mt) cc_final: 0.6081 (mt)
REVERT: B  852 LYS cc_start: 0.7209 (tttt) cc_final: 0.6922 (tttt)
REVERT: B  927 PHE cc_start: 0.5523 (m-10) cc_final: 0.5312 (m-10)
REVERT: B  977 TRP cc_start: 0.5308 (t60) cc_final: 0.4933 (t-100)
  outliers start: 27
  outliers final: 10
  residues processed: 238
  average time/residue: 0.6677
  time to fit residues: 170.9545
Evaluate side-chains
  223 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 211
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 LYS
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  796 ILE
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  998 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 81 optimal weight:    0.4980
   chunk 101 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 49 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A  53 ASN
B1125 HIS
B1126 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.183381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.168951 restraints weight = 15294.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.4218 rms_B_bonded: 1.73
r_work: 0.4134 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4004 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11459  Z= 0.183
  Angle     :  0.613   7.615  15546  Z= 0.316
  Chirality :  0.044   0.158   1752
  Planarity :  0.005   0.048   2032
  Dihedral  :  4.928  24.897   1580
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.24 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.22), residues: 1429
  helix:  0.67 (0.19), residues: 768
  sheet: -1.27 (0.42), residues: 147
  loop : -1.32 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 696 
 TYR   0.037   0.002   TYR B 874 
 PHE   0.021   0.002   PHE B 106 
 TRP   0.012   0.002   TRP B  35 
 HIS   0.007   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (11459)
  covalent geometry    : angle       0.61346 (15546)
  hydrogen bonds       : bond        0.04275 (  605)
  hydrogen bonds       : angle       5.09009 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 214
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.1211 (tpp) cc_final: 0.1008 (tpp)
REVERT: A  179 GLN cc_start: 0.7247 (mt0) cc_final: 0.7017 (mm110)
REVERT: B   35 TRP cc_start: 0.7312 (OUTLIER) cc_final: 0.6687 (m-10)
REVERT: B  322 ASN cc_start: 0.7543 (m-40) cc_final: 0.7148 (m-40)
REVERT: B  525 TRP cc_start: 0.7526 (p90) cc_final: 0.7275 (p90)
REVERT: B  602 PHE cc_start: 0.8254 (t80) cc_final: 0.8001 (t80)
REVERT: B  647 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6517 (mtmm)
REVERT: B  852 LYS cc_start: 0.7220 (tttt) cc_final: 0.6948 (tttt)
REVERT: B  927 PHE cc_start: 0.5607 (m-10) cc_final: 0.5375 (m-10)
  outliers start: 30
  outliers final: 9
  residues processed: 225
  average time/residue: 0.7146
  time to fit residues: 172.6188
Evaluate side-chains
  223 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 212
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  958 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 135 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 124 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.181565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.167194 restraints weight = 15348.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 1.74
r_work: 0.4111 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3980 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11459  Z= 0.231
  Angle     :  0.651  10.091  15546  Z= 0.334
  Chirality :  0.046   0.164   1752
  Planarity :  0.006   0.057   2032
  Dihedral  :  5.044  23.310   1578
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.92 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.22), residues: 1429
  helix:  0.49 (0.18), residues: 760
  sheet: -1.30 (0.43), residues: 147
  loop : -1.40 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 696 
 TYR   0.051   0.003   TYR B 874 
 PHE   0.024   0.002   PHE B 106 
 TRP   0.014   0.002   TRP B  35 
 HIS   0.009   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (11459)
  covalent geometry    : angle       0.65086 (15546)
  hydrogen bonds       : bond        0.04488 (  605)
  hydrogen bonds       : angle       5.21634 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 211
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.1027 (tpp) cc_final: 0.0824 (tpp)
REVERT: A  179 GLN cc_start: 0.7349 (mt0) cc_final: 0.7040 (mm110)
REVERT: A  203 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7425 (ttm-80)
REVERT: B   35 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6769 (m-10)
REVERT: B  359 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8020 (pp)
REVERT: B  525 TRP cc_start: 0.7602 (p90) cc_final: 0.7335 (p90)
REVERT: B  602 PHE cc_start: 0.8273 (t80) cc_final: 0.8017 (t80)
REVERT: B  647 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6497 (mttp)
REVERT: B  852 LYS cc_start: 0.7222 (tttt) cc_final: 0.6946 (tttt)
REVERT: B  927 PHE cc_start: 0.5813 (m-10) cc_final: 0.5600 (m-10)
REVERT: B  979 MET cc_start: 0.6380 (mtt) cc_final: 0.4936 (mpt)
REVERT: B  983 ARG cc_start: 0.6649 (ttp80) cc_final: 0.6362 (ttp-110)
  outliers start: 32
  outliers final: 16
  residues processed: 224
  average time/residue: 0.6734
  time to fit residues: 162.1380
Evaluate side-chains
  224 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 205
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  796 ILE
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1139 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0980
   chunk 50 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 132 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.184221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.169991 restraints weight = 15286.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 1.74
r_work: 0.4137 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4008 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11459  Z= 0.159
  Angle     :  0.605  10.964  15546  Z= 0.311
  Chirality :  0.043   0.155   1752
  Planarity :  0.005   0.051   2032
  Dihedral  :  4.861  23.265   1578
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.01 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.22), residues: 1429
  helix:  0.65 (0.19), residues: 769
  sheet: -1.36 (0.42), residues: 148
  loop : -1.27 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 360 
 TYR   0.051   0.002   TYR B 874 
 PHE   0.023   0.002   PHE B 106 
 TRP   0.012   0.001   TRP B  35 
 HIS   0.006   0.001   HIS B 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (11459)
  covalent geometry    : angle       0.60474 (15546)
  hydrogen bonds       : bond        0.04014 (  605)
  hydrogen bonds       : angle       5.05267 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.0981 (tpp) cc_final: 0.0771 (tpp)
REVERT: A  179 GLN cc_start: 0.7384 (mt0) cc_final: 0.7074 (mm110)
REVERT: A  203 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7411 (ttm-80)
REVERT: B   35 TRP cc_start: 0.7341 (OUTLIER) cc_final: 0.6745 (m-10)
REVERT: B  359 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7942 (pp)
REVERT: B  525 TRP cc_start: 0.7590 (p90) cc_final: 0.7294 (p90)
REVERT: B  602 PHE cc_start: 0.8246 (t80) cc_final: 0.7998 (t80)
REVERT: B  852 LYS cc_start: 0.7195 (tttt) cc_final: 0.6894 (tttt)
REVERT: B  867 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7933 (t)
REVERT: B  927 PHE cc_start: 0.5697 (m-10) cc_final: 0.5477 (m-10)
  outliers start: 32
  outliers final: 15
  residues processed: 224
  average time/residue: 0.6785
  time to fit residues: 163.3415
Evaluate side-chains
  219 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 201
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  744 LEU
Chi-restraints excluded: chain B residue  867 THR
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue 1023 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 135 optimal weight:    0.4980
   chunk 106 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 119 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 139 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.181290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.166964 restraints weight = 15315.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 1.74
r_work: 0.4108 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3977 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  11459  Z= 0.240
  Angle     :  0.679  11.503  15546  Z= 0.347
  Chirality :  0.047   0.283   1752
  Planarity :  0.006   0.061   2032
  Dihedral  :  5.054  23.948   1578
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.51 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.22), residues: 1429
  helix:  0.47 (0.18), residues: 764
  sheet: -1.23 (0.42), residues: 152
  loop : -1.34 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 360 
 TYR   0.050   0.003   TYR B 874 
 PHE   0.026   0.002   PHE B 106 
 TRP   0.016   0.002   TRP A 232 
 HIS   0.009   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (11459)
  covalent geometry    : angle       0.67918 (15546)
  hydrogen bonds       : bond        0.04507 (  605)
  hydrogen bonds       : angle       5.21938 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 205
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 GLN cc_start: 0.7496 (mt0) cc_final: 0.7159 (mm110)
REVERT: A  203 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7489 (ttm-80)
REVERT: A  223 GLU cc_start: 0.6417 (tp30) cc_final: 0.6215 (tp30)
REVERT: B   35 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6804 (m-10)
REVERT: B  359 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7952 (pp)
REVERT: B  525 TRP cc_start: 0.7618 (p90) cc_final: 0.7337 (p90)
REVERT: B  602 PHE cc_start: 0.8282 (t80) cc_final: 0.8024 (t80)
REVERT: B  647 LYS cc_start: 0.6843 (mttp) cc_final: 0.6623 (mptp)
REVERT: B  852 LYS cc_start: 0.7190 (tttt) cc_final: 0.6919 (tttt)
  outliers start: 32
  outliers final: 18
  residues processed: 218
  average time/residue: 0.6483
  time to fit residues: 152.0639
Evaluate side-chains
  218 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 198
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  530 ILE
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  796 ILE
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1064 HIS
Chi-restraints excluded: chain B residue 1139 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 137 optimal weight:    0.0070
   chunk 108 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0980
   chunk 76 optimal weight:    0.7980
   chunk 136 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.3598

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

Flipped N/Q/H residues before XYZ refinement:
B 146 GLN
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.184393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.170229 restraints weight = 15349.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4229 rms_B_bonded: 1.73
r_work: 0.4147 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4020 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6758
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11459  Z= 0.148
  Angle     :  0.622  13.322  15546  Z= 0.316
  Chirality :  0.044   0.242   1752
  Planarity :  0.005   0.079   2032
  Dihedral  :  4.791  23.099   1578
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.02 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.22), residues: 1429
  helix:  0.76 (0.19), residues: 770
  sheet: -1.25 (0.42), residues: 153
  loop : -1.25 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 360 
 TYR   0.047   0.002   TYR B 874 
 PHE   0.024   0.002   PHE B 106 
 TRP   0.012   0.001   TRP A 232 
 HIS   0.006   0.001   HIS B 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (11459)
  covalent geometry    : angle       0.62237 (15546)
  hydrogen bonds       : bond        0.03881 (  605)
  hydrogen bonds       : angle       5.01220 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 207
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLN cc_start: 0.7431 (mt0) cc_final: 0.7080 (mm110)
REVERT: A  203 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7438 (ttm-80)
REVERT: B   35 TRP cc_start: 0.7285 (OUTLIER) cc_final: 0.6685 (m-10)
REVERT: B  312 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.7103 (mtt90)
REVERT: B  359 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7897 (pp)
REVERT: B  472 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6748 (m-30)
REVERT: B  525 TRP cc_start: 0.7546 (p90) cc_final: 0.7278 (p90)
REVERT: B  602 PHE cc_start: 0.8248 (t80) cc_final: 0.8035 (t80)
REVERT: B  852 LYS cc_start: 0.7133 (tttt) cc_final: 0.6880 (tttt)
REVERT: B  977 TRP cc_start: 0.5156 (t60) cc_final: 0.4603 (t60)
  outliers start: 28
  outliers final: 14
  residues processed: 221
  average time/residue: 0.6343
  time to fit residues: 150.9071
Evaluate side-chains
  215 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  874 TYR
Chi-restraints excluded: chain B residue 1064 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 139 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 126 optimal weight:    0.0670
   chunk 100 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.182042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.168057 restraints weight = 15276.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 1.68
r_work: 0.4127 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4000 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11459  Z= 0.212
  Angle     :  0.672  12.727  15546  Z= 0.340
  Chirality :  0.046   0.217   1752
  Planarity :  0.005   0.055   2032
  Dihedral  :  4.941  24.112   1578
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.11 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.22), residues: 1429
  helix:  0.55 (0.18), residues: 771
  sheet: -1.20 (0.42), residues: 152
  loop : -1.30 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 837 
 TYR   0.050   0.003   TYR B 874 
 PHE   0.025   0.002   PHE B 106 
 TRP   0.017   0.002   TRP A 232 
 HIS   0.008   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (11459)
  covalent geometry    : angle       0.67210 (15546)
  hydrogen bonds       : bond        0.04262 (  605)
  hydrogen bonds       : angle       5.12449 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 198
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLN cc_start: 0.7462 (mt0) cc_final: 0.7143 (mm110)
REVERT: A  203 ARG cc_start: 0.7708 (ttm110) cc_final: 0.7433 (ttm-80)
REVERT: B   35 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.6730 (m-10)
REVERT: B  359 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8066 (pp)
REVERT: B  472 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6788 (m-30)
REVERT: B  525 TRP cc_start: 0.7557 (p90) cc_final: 0.7308 (p90)
REVERT: B  602 PHE cc_start: 0.8267 (t80) cc_final: 0.8050 (t80)
REVERT: B  852 LYS cc_start: 0.7136 (tttt) cc_final: 0.6889 (tttt)
REVERT: B 1166 LEU cc_start: 0.7483 (mp) cc_final: 0.7250 (mt)
  outliers start: 30
  outliers final: 18
  residues processed: 214
  average time/residue: 0.6839
  time to fit residues: 157.3586
Evaluate side-chains
  212 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  973 TYR
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1064 HIS
Chi-restraints excluded: chain B residue 1133 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 136 optimal weight:    0.4980
   chunk 96 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 128 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.181847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.167587 restraints weight = 15276.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 1.73
r_work: 0.4118 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3988 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11459  Z= 0.221
  Angle     :  0.694  13.329  15546  Z= 0.350
  Chirality :  0.047   0.231   1752
  Planarity :  0.006   0.054   2032
  Dihedral  :  5.028  24.236   1578
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.61 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.22), residues: 1429
  helix:  0.48 (0.18), residues: 771
  sheet: -1.23 (0.42), residues: 148
  loop : -1.37 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 312 
 TYR   0.054   0.003   TYR B 874 
 PHE   0.025   0.002   PHE B 106 
 TRP   0.020   0.002   TRP A 232 
 HIS   0.008   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (11459)
  covalent geometry    : angle       0.69435 (15546)
  hydrogen bonds       : bond        0.04314 (  605)
  hydrogen bonds       : angle       5.20323 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 194
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLN cc_start: 0.7439 (mt0) cc_final: 0.7087 (mm110)
REVERT: A  203 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7478 (ttm-80)
REVERT: B   35 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.6763 (m-10)
REVERT: B  472 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6818 (m-30)
REVERT: B  525 TRP cc_start: 0.7621 (p90) cc_final: 0.7324 (p90)
REVERT: B  602 PHE cc_start: 0.8298 (t80) cc_final: 0.8089 (t80)
REVERT: B  852 LYS cc_start: 0.7165 (tttt) cc_final: 0.6903 (tttt)
REVERT: B 1128 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5880 (mt)
REVERT: B 1166 LEU cc_start: 0.7563 (mp) cc_final: 0.7329 (mt)
  outliers start: 31
  outliers final: 21
  residues processed: 209
  average time/residue: 0.6853
  time to fit residues: 153.6572
Evaluate side-chains
  215 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  548 LYS
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  874 TYR
Chi-restraints excluded: chain B residue  958 THR
Chi-restraints excluded: chain B residue  973 TYR
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1064 HIS
Chi-restraints excluded: chain B residue 1128 LEU
Chi-restraints excluded: chain B residue 1133 THR
Chi-restraints excluded: chain B residue 1139 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 134 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.3980
   chunk 121 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 140 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 116 optimal weight:    1.9990
   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  92 ASN
** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.182478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.168494 restraints weight = 15273.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 1.68
r_work: 0.4130 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4005 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11459  Z= 0.198
  Angle     :  0.686  13.796  15546  Z= 0.345
  Chirality :  0.046   0.237   1752
  Planarity :  0.005   0.052   2032
  Dihedral  :  4.982  24.067   1578
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.69 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.22), residues: 1429
  helix:  0.54 (0.18), residues: 770
  sheet: -1.23 (0.42), residues: 148
  loop : -1.35 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 837 
 TYR   0.053   0.003   TYR B 874 
 PHE   0.027   0.002   PHE B 106 
 TRP   0.020   0.002   TRP A 232 
 HIS   0.007   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (11459)
  covalent geometry    : angle       0.68642 (15546)
  hydrogen bonds       : bond        0.04178 (  605)
  hydrogen bonds       : angle       5.15315 ( 1776)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLN cc_start: 0.7435 (mt0) cc_final: 0.7105 (mm110)
REVERT: A  203 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7429 (ttm-80)
REVERT: B   35 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.6727 (m-10)
REVERT: B  472 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6787 (m-30)
REVERT: B  525 TRP cc_start: 0.7566 (p90) cc_final: 0.7325 (p90)
REVERT: B  602 PHE cc_start: 0.8246 (t80) cc_final: 0.8031 (t80)
REVERT: B  852 LYS cc_start: 0.7115 (tttt) cc_final: 0.6867 (tttt)
REVERT: B 1166 LEU cc_start: 0.7489 (mp) cc_final: 0.7270 (mt)
  outliers start: 28
  outliers final: 20
  residues processed: 212
  average time/residue: 0.6939
  time to fit residues: 158.0168
Evaluate side-chains
  218 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  548 LYS
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  684 HIS
Chi-restraints excluded: chain B residue  767 THR
Chi-restraints excluded: chain B residue  874 TYR
Chi-restraints excluded: chain B residue  973 TYR
Chi-restraints excluded: chain B residue 1023 LEU
Chi-restraints excluded: chain B residue 1064 HIS
Chi-restraints excluded: chain B residue 1133 THR
Chi-restraints excluded: chain B residue 1139 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 118 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 128 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   chunk 68 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1125 HIS
B1158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.183297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.169035 restraints weight = 15382.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.4216 rms_B_bonded: 1.74
r_work: 0.4133 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4004 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6789
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11459  Z= 0.178
  Angle     :  0.668  13.091  15546  Z= 0.335
  Chirality :  0.045   0.207   1752
  Planarity :  0.005   0.052   2032
  Dihedral  :  4.925  23.877   1578
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 22.11 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.22), residues: 1429
  helix:  0.63 (0.19), residues: 770
  sheet: -1.29 (0.42), residues: 150
  loop : -1.34 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 360 
 TYR   0.052   0.003   TYR B 874 
 PHE   0.026   0.002   PHE B 106 
 TRP   0.022   0.002   TRP A 232 
 HIS   0.006   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (11459)
  covalent geometry    : angle       0.66847 (15546)
  hydrogen bonds       : bond        0.04030 (  605)
  hydrogen bonds       : angle       5.10632 ( 1776)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5156.11 seconds
wall clock time: 88 minutes 24.49 seconds (5304.49 seconds total)