Starting phenix.real_space_refine
on Tue Sep 24 07:39:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/09_2024/7tof_26031.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/09_2024/7tof_26031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/09_2024/7tof_26031.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/09_2024/7tof_26031.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/09_2024/7tof_26031.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/09_2024/7tof_26031.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.104
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      40      5.16       5
     C    4838      2.51       5
     N    1318      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 7588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3794
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3794
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   GLU A 504 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  GLU A 504 " occ=0.50
    residue:
      pdb=" N   GLU B 504 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  GLU B 504 " occ=0.50
  Time building chain proxies: 4.60, per 1000 atoms: 0.61
  Number of scatterers: 7588
  At special positions: 0
  Unit cell: (73.04, 80.51, 135.29, 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      40     16.00
     O    1392      8.00
     N    1318      7.00
     C    4838      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 937.0 milliseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 6 sheets defined
      42.3% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 47
    Processing helix  chain 'A' and resid 48 through 58
      removed outlier: 3.822A  pdb=" N   ASP A  58 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      Proline residue:  A  86  - end of helix
      removed outlier: 3.856A  pdb=" N   LYS A  89 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 103
    Processing helix  chain 'A' and resid 114 through 127
      removed outlier: 3.768A  pdb=" N   TYR A 118 " --> pdb=" O   ASP A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 146 through 158
      removed outlier: 3.996A  pdb=" N   LYS A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 191
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 206 through 217
      removed outlier: 3.745A  pdb=" N   MET A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 251
      removed outlier: 4.168A  pdb=" N   PHE A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 246 through 251'
    Processing helix  chain 'A' and resid 253 through 259
      removed outlier: 4.378A  pdb=" N   ARG A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 273
    Processing helix  chain 'A' and resid 280 through 294
    Processing helix  chain 'A' and resid 299 through 301
      No H-bonds generated for 'chain 'A' and resid 299 through 301'
    Processing helix  chain 'A' and resid 316 through 320
      removed outlier: 3.621A  pdb=" N   THR A 319 " --> pdb=" O   GLY A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
    Processing helix  chain 'A' and resid 454 through 476
      removed outlier: 3.557A  pdb=" N   PHE A 465 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
      Proline residue:  A 467  - end of helix
    Processing helix  chain 'A' and resid 489 through 500
      removed outlier: 4.037A  pdb=" N   ASP A 493 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 47
    Processing helix  chain 'B' and resid 47 through 58
      removed outlier: 3.605A  pdb=" N   THR B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASP B  58 " --> pdb=" O   TRP B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 85
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 91 through 93
      No H-bonds generated for 'chain 'B' and resid 91 through 93'
    Processing helix  chain 'B' and resid 94 through 103
      removed outlier: 3.554A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 127
      removed outlier: 3.591A  pdb=" N   TYR B 118 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 145
      No H-bonds generated for 'chain 'B' and resid 143 through 145'
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 3.895A  pdb=" N   LYS B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 191
    Processing helix  chain 'B' and resid 192 through 194
      No H-bonds generated for 'chain 'B' and resid 192 through 194'
    Processing helix  chain 'B' and resid 206 through 217
      removed outlier: 4.019A  pdb=" N   MET B 212 " --> pdb=" O   VAL B 208 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 259
    Processing helix  chain 'B' and resid 262 through 273
    Processing helix  chain 'B' and resid 280 through 294
    Processing helix  chain 'B' and resid 299 through 301
      No H-bonds generated for 'chain 'B' and resid 299 through 301'
    Processing helix  chain 'B' and resid 316 through 320
    Processing helix  chain 'B' and resid 435 through 447
      removed outlier: 3.571A  pdb=" N   ARG B 439 " --> pdb=" O   ASP B 435 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 476
      Proline residue:  B 467  - end of helix
    Processing helix  chain 'B' and resid 489 through 500
      removed outlier: 4.054A  pdb=" N   ASP B 493 " --> pdb=" O   PRO B 489 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109
      removed outlier: 8.558A  pdb=" N   SER A 106 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ILE A  67 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL A 108 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   GLY A  69 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A  33 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR A 139 " --> pdb=" O   ILE A  33 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ILE A  35 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   TYR A 197 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 167 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 421
      removed outlier: 8.494A  pdb=" N   ILE A 355 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   VAL A 233 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ARG A 357 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   LEU A 235 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLY A 359 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   PHE A 237 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   CYS A 358 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 9.491A  pdb=" N   ILE A 480 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU A 305 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   TYR A 482 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   GLN A 307 " --> pdb=" O   TYR A 482 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 407
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 109
      removed outlier: 6.221A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   TYR B 139 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE B  35 " --> pdb=" O   TYR B 139 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B 166 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE B 168 " --> pdb=" O   PHE B 138 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   TYR B 197 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE B 167 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 421
      removed outlier: 3.534A  pdb=" N   LEU B 420 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ALA B 367 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 8.612A  pdb=" N   ILE B 355 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   VAL B 233 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ARG B 357 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   LEU B 235 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   GLY B 359 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   PHE B 237 " --> pdb=" O   GLY B 359 " (cutoff:3.500A)
      removed outlier: 9.297A  pdb=" N   ILE B 480 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   LEU B 305 " --> pdb=" O   ILE B 480 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   TYR B 482 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN B 307 " --> pdb=" O   TYR B 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 405 through 407

    295 hydrogen bonds defined for protein.
    846 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: 2.03

  Time building geometry restraints manager: 2.00 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: 2518
        1.34 -     1.46: 1498
        1.46 -     1.58: 3684
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 7766
  Sorted by residual:
  bond pdb=" CB  TRP B 225 "
       pdb=" CG  TRP B 225 "
    ideal  model  delta    sigma   weight residual
    1.498  1.461  0.037 3.10e-02 1.04e+03 1.44e+00
  bond pdb=" CB  GLU B 156 "
       pdb=" CG  GLU B 156 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.56e-01
  bond pdb=" CA  LYS B 403 "
       pdb=" C   LYS B 403 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.010 1.10e-02 8.26e+03 8.06e-01
  bond pdb=" CG  LEU A 235 "
       pdb=" CD1 LEU A 235 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.01e-01
  bond pdb=" CA  ILE B  36 "
       pdb=" CB  ILE B  36 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.11e-02 8.12e+03 6.37e-01
  ... (remaining 7761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 10025
        1.26 -     2.52: 387
        2.52 -     3.78: 68
        3.78 -     5.04: 16
        5.04 -     6.30: 6
  Bond angle restraints: 10502
  Sorted by residual:
  angle pdb=" C   TRP A 462 "
        pdb=" N   ARG A 463 "
        pdb=" CA  ARG A 463 "
      ideal   model   delta    sigma   weight residual
     121.14  116.26    4.88 1.75e+00 3.27e-01 7.78e+00
  angle pdb=" N   SER A  29 "
        pdb=" CA  SER A  29 "
        pdb=" C   SER A  29 "
      ideal   model   delta    sigma   weight residual
     113.43  110.35    3.08 1.26e+00 6.30e-01 5.96e+00
  angle pdb=" C   LEU B 214 "
        pdb=" N   ARG B 215 "
        pdb=" CA  ARG B 215 "
      ideal   model   delta    sigma   weight residual
     120.68  124.78   -4.10 1.70e+00 3.46e-01 5.81e+00
  angle pdb=" N   LYS B 205 "
        pdb=" CA  LYS B 205 "
        pdb=" CB  LYS B 205 "
      ideal   model   delta    sigma   weight residual
     113.65  110.11    3.54 1.47e+00 4.63e-01 5.81e+00
  angle pdb=" N   SER B  29 "
        pdb=" CA  SER B  29 "
        pdb=" C   SER B  29 "
      ideal   model   delta    sigma   weight residual
     113.43  110.51    2.92 1.26e+00 6.30e-01 5.35e+00
  ... (remaining 10497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 4125
       16.83 -    33.66: 421
       33.66 -    50.50: 86
       50.50 -    67.33: 25
       67.33 -    84.16: 17
  Dihedral angle restraints: 4674
    sinusoidal: 1944
      harmonic: 2730
  Sorted by residual:
  dihedral pdb=" CA  ASN A 218 "
           pdb=" C   ASN A 218 "
           pdb=" N   ARG A 219 "
           pdb=" CA  ARG A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.23   18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ARG B 227 "
           pdb=" C   ARG B 227 "
           pdb=" N   ASP B 228 "
           pdb=" CA  ASP B 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL A 259 "
           pdb=" C   VAL A 259 "
           pdb=" N   MET A 260 "
           pdb=" CA  MET A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 4671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 617
       0.028 -    0.056: 300
       0.056 -    0.084: 117
       0.084 -    0.112: 70
       0.112 -    0.140: 20
  Chirality restraints: 1124
  Sorted by residual:
  chirality pdb=" CA  VAL B 369 "
            pdb=" N   VAL B 369 "
            pdb=" C   VAL B 369 "
            pdb=" CB  VAL B 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  VAL B 400 "
            pdb=" N   VAL B 400 "
            pdb=" C   VAL B 400 "
            pdb=" CB  VAL B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  VAL A 369 "
            pdb=" N   VAL A 369 "
            pdb=" C   VAL A 369 "
            pdb=" CB  VAL A 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1121 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 480 "   -0.056 5.00e-02 4.00e+02   8.51e-02 1.16e+01
        pdb=" N   PRO A 481 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 222 "   -0.051 5.00e-02 4.00e+02   7.75e-02 9.61e+00
        pdb=" N   PRO A 223 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 352 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO A 353 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 353 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 353 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 229
        2.71 -     3.26: 7699
        3.26 -     3.81: 12707
        3.81 -     4.35: 15586
        4.35 -     4.90: 26279
  Nonbonded interactions: 62500
  Sorted by model distance:
  nonbonded pdb=" O   TRP B 462 "
            pdb=" OG1 THR B 466 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   ALA A 115 "
            pdb=" NE2 GLN A 119 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OE1 GLU A 460 "
            pdb=" NH1 ARG A 463 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" NH1 ARG B 175 "
            pdb=" O   GLU B 252 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OG  SER A 296 "
            pdb=" OE2 GLU A 345 "
     model   vdw
     2.245 3.040
  ... (remaining 62495 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     19.600
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6278
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7766  Z= 0.215
  Angle     :  0.602   6.301  10502  Z= 0.326
  Chirality :  0.044   0.140   1124
  Planarity :  0.005   0.085   1374
  Dihedral  : 15.200  84.160   2914
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.24 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.28), residues: 930
  helix:  0.31 (0.30), residues: 344
  sheet: -1.18 (0.39), residues: 162
  loop : -0.52 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 164 
 HIS   0.004   0.001   HIS B 155 
 PHE   0.024   0.002   PHE A 102 
 TYR   0.014   0.002   TYR B 484 
 ARG   0.006   0.001   ARG B 357 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7477 (ptpp) cc_final: 0.7265 (ptpp)
REVERT: B   87 PHE cc_start: 0.7357 (m-10) cc_final: 0.6997 (m-80)
REVERT: B  137 LEU cc_start: 0.7398 (tt) cc_final: 0.7152 (tt)
REVERT: B  345 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6197 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1889
  time to fit residues: 39.8772
Evaluate side-chains
  114 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 GLN
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 GLN
** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
B 153 ASN
** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7766  Z= 0.319
  Angle     :  0.667   8.027  10502  Z= 0.342
  Chirality :  0.047   0.168   1124
  Planarity :  0.005   0.062   1374
  Dihedral  :  4.790  21.237   1032
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.00 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.28), residues: 930
  helix:  0.41 (0.30), residues: 328
  sheet: -1.20 (0.38), residues: 156
  loop : -0.71 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 164 
 HIS   0.005   0.001   HIS B 124 
 PHE   0.028   0.002   PHE A 102 
 TYR   0.017   0.002   TYR A 118 
 ARG   0.006   0.001   ARG B 357 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LEU cc_start: 0.4611 (mt) cc_final: 0.4297 (mt)
REVERT: B   87 PHE cc_start: 0.7388 (m-10) cc_final: 0.7005 (m-80)
REVERT: B  120 ARG cc_start: 0.7396 (tmm-80) cc_final: 0.7099 (ttp-110)
REVERT: B  170 GLU cc_start: 0.6699 (tp30) cc_final: 0.6449 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1701
  time to fit residues: 35.4204
Evaluate side-chains
  129 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 56 optimal weight:   20.0000
   chunk 23 optimal weight:    0.6980
   chunk 83 optimal weight:    0.4980
   chunk 90 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 165 ASN
B 388 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6339
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7766  Z= 0.183
  Angle     :  0.589   8.006  10502  Z= 0.300
  Chirality :  0.044   0.181   1124
  Planarity :  0.004   0.052   1374
  Dihedral  :  4.531  18.684   1032
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.32 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.28), residues: 930
  helix:  0.58 (0.30), residues: 328
  sheet: -1.05 (0.37), residues: 168
  loop : -0.70 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 349 
 HIS   0.007   0.001   HIS A 451 
 PHE   0.022   0.001   PHE A 102 
 TYR   0.015   0.002   TYR B 484 
 ARG   0.006   0.000   ARG B 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 GLU cc_start: 0.7776 (mp0) cc_final: 0.6740 (tt0)
REVERT: B   87 PHE cc_start: 0.7427 (m-10) cc_final: 0.7144 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 148
  average time/residue: 0.1698
  time to fit residues: 35.1777
Evaluate side-chains
  129 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 74 optimal weight:   20.0000
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7766  Z= 0.281
  Angle     :  0.627   7.912  10502  Z= 0.319
  Chirality :  0.046   0.253   1124
  Planarity :  0.005   0.054   1374
  Dihedral  :  4.723  22.256   1032
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.37 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 930
  helix:  0.27 (0.29), residues: 342
  sheet: -1.23 (0.37), residues: 174
  loop : -0.66 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 349 
 HIS   0.005   0.001   HIS A 451 
 PHE   0.020   0.002   PHE A 102 
 TYR   0.020   0.002   TYR A 401 
 ARG   0.007   0.001   ARG A 439 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ASP cc_start: 0.7146 (m-30) cc_final: 0.6760 (m-30)
REVERT: A  315 GLU cc_start: 0.7787 (mp0) cc_final: 0.6898 (tt0)
REVERT: B   99 GLU cc_start: 0.7308 (mp0) cc_final: 0.7096 (pm20)
REVERT: B  170 GLU cc_start: 0.6640 (tp30) cc_final: 0.6251 (tp30)
  outliers start: 20
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1847
  time to fit residues: 38.2616
Evaluate side-chains
  138 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 75 optimal weight:   30.0000
   chunk 61 optimal weight:   20.0000
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:   40.0000
   chunk 79 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0770
   overall best weight:    4.2146

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  64 ASN
B 124 HIS
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   7766  Z= 0.377
  Angle     :  0.710   9.785  10502  Z= 0.362
  Chirality :  0.049   0.341   1124
  Planarity :  0.005   0.059   1374
  Dihedral  :  5.174  26.221   1032
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.07 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.28), residues: 930
  helix:  0.02 (0.29), residues: 330
  sheet: -1.63 (0.35), residues: 188
  loop : -0.83 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 349 
 HIS   0.007   0.002   HIS B 263 
 PHE   0.023   0.003   PHE A 253 
 TYR   0.020   0.003   TYR A 484 
 ARG   0.006   0.001   ARG B  81 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ASP cc_start: 0.7424 (m-30) cc_final: 0.7171 (m-30)
REVERT: A  315 GLU cc_start: 0.7973 (mp0) cc_final: 0.7193 (tt0)
REVERT: B   99 GLU cc_start: 0.7350 (mp0) cc_final: 0.7148 (mp0)
REVERT: B  170 GLU cc_start: 0.6864 (tp30) cc_final: 0.6652 (tp30)
REVERT: B  273 MET cc_start: 0.4622 (ptt) cc_final: 0.4213 (ptt)
  outliers start: 27
  outliers final: 17
  residues processed: 143
  average time/residue: 0.1764
  time to fit residues: 35.2587
Evaluate side-chains
  141 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  499 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0000
   chunk 46 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7766  Z= 0.179
  Angle     :  0.599   8.398  10502  Z= 0.305
  Chirality :  0.045   0.219   1124
  Planarity :  0.004   0.059   1374
  Dihedral  :  4.647  20.312   1032
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.00 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.28), residues: 930
  helix:  0.25 (0.29), residues: 342
  sheet: -1.44 (0.36), residues: 184
  loop : -0.67 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 349 
 HIS   0.007   0.001   HIS A 451 
 PHE   0.022   0.002   PHE A 102 
 TYR   0.016   0.002   TYR A 343 
 ARG   0.003   0.000   ARG B  81 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ASP cc_start: 0.7133 (m-30) cc_final: 0.6911 (m-30)
REVERT: A  315 GLU cc_start: 0.7863 (mp0) cc_final: 0.7164 (tt0)
REVERT: A  439 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7111 (mmm-85)
REVERT: B  170 GLU cc_start: 0.6627 (tp30) cc_final: 0.6197 (tp30)
  outliers start: 21
  outliers final: 15
  residues processed: 147
  average time/residue: 0.1845
  time to fit residues: 38.1093
Evaluate side-chains
  134 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  499 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 50 optimal weight:    8.9990
   chunk 65 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 55 optimal weight:   20.0000
   chunk 54 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 GLN
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7766  Z= 0.218
  Angle     :  0.613   8.824  10502  Z= 0.313
  Chirality :  0.046   0.240   1124
  Planarity :  0.004   0.058   1374
  Dihedral  :  4.688  19.975   1032
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.73 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.28), residues: 930
  helix:  0.26 (0.29), residues: 342
  sheet: -1.16 (0.38), residues: 176
  loop : -0.70 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 349 
 HIS   0.007   0.001   HIS A 451 
 PHE   0.022   0.002   PHE A 102 
 TYR   0.016   0.002   TYR A 343 
 ARG   0.008   0.000   ARG B 120 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7494 (tppt) cc_final: 0.7154 (tppt)
REVERT: A  313 ASP cc_start: 0.7192 (m-30) cc_final: 0.6971 (m-30)
REVERT: A  315 GLU cc_start: 0.7893 (mp0) cc_final: 0.7192 (tt0)
REVERT: A  439 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7029 (mmm160)
REVERT: B  170 GLU cc_start: 0.6772 (tp30) cc_final: 0.6555 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 141
  average time/residue: 0.1783
  time to fit residues: 34.9814
Evaluate side-chains
  141 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  499 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 56 optimal weight:   30.0000
   chunk 60 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 69 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0470
   chunk 77 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.7284

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7766  Z= 0.218
  Angle     :  0.630   8.640  10502  Z= 0.321
  Chirality :  0.047   0.240   1124
  Planarity :  0.004   0.056   1374
  Dihedral  :  4.674  19.738   1032
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.61 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.28), residues: 930
  helix:  0.36 (0.30), residues: 342
  sheet: -1.15 (0.38), residues: 174
  loop : -0.67 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 349 
 HIS   0.007   0.001   HIS B 186 
 PHE   0.021   0.002   PHE A 102 
 TYR   0.017   0.002   TYR A 249 
 ARG   0.005   0.000   ARG B 104 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7436 (tppt) cc_final: 0.7191 (tppt)
REVERT: A  313 ASP cc_start: 0.7260 (m-30) cc_final: 0.7045 (m-30)
REVERT: A  315 GLU cc_start: 0.7900 (mp0) cc_final: 0.7189 (tt0)
REVERT: A  439 ARG cc_start: 0.7542 (mmm160) cc_final: 0.6926 (mmm160)
REVERT: B  170 GLU cc_start: 0.6728 (tp30) cc_final: 0.6515 (tp30)
REVERT: B  193 GLU cc_start: 0.5400 (tp30) cc_final: 0.5169 (tp30)
  outliers start: 26
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1679
  time to fit residues: 34.3439
Evaluate side-chains
  140 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 35 optimal weight:    0.2980
   chunk 64 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7766  Z= 0.237
  Angle     :  0.661   9.865  10502  Z= 0.335
  Chirality :  0.048   0.321   1124
  Planarity :  0.004   0.056   1374
  Dihedral  :  4.732  19.809   1032
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.71 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.28), residues: 930
  helix:  0.36 (0.30), residues: 342
  sheet: -1.24 (0.38), residues: 176
  loop : -0.67 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 164 
 HIS   0.007   0.001   HIS A 451 
 PHE   0.025   0.002   PHE A 253 
 TYR   0.017   0.002   TYR A 343 
 ARG   0.008   0.001   ARG B 246 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ASP cc_start: 0.7312 (m-30) cc_final: 0.7092 (m-30)
REVERT: A  315 GLU cc_start: 0.7893 (mp0) cc_final: 0.7191 (tt0)
REVERT: A  439 ARG cc_start: 0.7487 (mmm160) cc_final: 0.6824 (mmm160)
REVERT: B   99 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7192 (pm20)
REVERT: B  170 GLU cc_start: 0.6793 (tp30) cc_final: 0.6579 (tp30)
REVERT: B  193 GLU cc_start: 0.5451 (tp30) cc_final: 0.5200 (tp30)
  outliers start: 29
  outliers final: 25
  residues processed: 139
  average time/residue: 0.1677
  time to fit residues: 33.1357
Evaluate side-chains
  146 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  212 MET
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 56 optimal weight:   30.0000
   chunk 44 optimal weight:    0.0170
   chunk 57 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   overall best weight:    2.2022

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7766  Z= 0.250
  Angle     :  0.671   9.950  10502  Z= 0.342
  Chirality :  0.048   0.324   1124
  Planarity :  0.004   0.056   1374
  Dihedral  :  4.815  20.603   1032
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.32 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 930
  helix:  0.43 (0.30), residues: 334
  sheet: -1.32 (0.38), residues: 176
  loop : -0.74 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 349 
 HIS   0.008   0.001   HIS B 186 
 PHE   0.025   0.002   PHE A 253 
 TYR   0.018   0.002   TYR A 343 
 ARG   0.007   0.001   ARG B 246 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ASP cc_start: 0.7356 (m-30) cc_final: 0.7134 (m-30)
REVERT: A  315 GLU cc_start: 0.7914 (mp0) cc_final: 0.7204 (tt0)
REVERT: B   99 GLU cc_start: 0.7450 (pm20) cc_final: 0.7183 (pm20)
REVERT: B  170 GLU cc_start: 0.6794 (tp30) cc_final: 0.6338 (tp30)
  outliers start: 25
  outliers final: 21
  residues processed: 141
  average time/residue: 0.1662
  time to fit residues: 33.2738
Evaluate side-chains
  144 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 30 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0980
   chunk 64 optimal weight:    0.6980
   chunk 4 optimal weight:   20.0000
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
A 451 HIS
** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.217648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.186995 restraints weight = 10493.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.187186 restraints weight = 9899.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.189231 restraints weight = 7970.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4385 r_free = 0.4385    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4385 r_free = 0.4385    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7766  Z= 0.214
  Angle     :  0.659   9.625  10502  Z= 0.336
  Chirality :  0.047   0.292   1124
  Planarity :  0.005   0.077   1374
  Dihedral  :  4.703  19.516   1032
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.32 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.28), residues: 930
  helix:  0.40 (0.29), residues: 336
  sheet: -1.27 (0.38), residues: 174
  loop : -0.78 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 349 
 HIS   0.008   0.001   HIS A 451 
 PHE   0.024   0.002   PHE A 253 
 TYR   0.016   0.002   TYR A 343 
 ARG   0.017   0.001   ARG B 104 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1704.14 seconds
wall clock time: 31 minutes 15.02 seconds (1875.02 seconds total)