Starting phenix.real_space_refine
on Thu Mar 14 16:55:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whn_32505/03_2024/7whn_32505.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whn_32505/03_2024/7whn_32505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whn_32505/03_2024/7whn_32505.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whn_32505/03_2024/7whn_32505.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whn_32505/03_2024/7whn_32505.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whn_32505/03_2024/7whn_32505.pdb"
  }
  resolution = 3.3
  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=   0.005
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    5816      2.51       5
     N    1629      2.21       5
     O    1800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   45": "NH1" <-> "NH2"
    Residue "A ARG   47": "NH1" <-> "NH2"
    Residue "A ARG   57": "NH1" <-> "NH2"
    Residue "A ARG   62": "NH1" <-> "NH2"
    Residue "A GLU   71": "OE1" <-> "OE2"
    Residue "A GLU   91": "OE1" <-> "OE2"
    Residue "A ARG  129": "NH1" <-> "NH2"
    Residue "A GLU  145": "OE1" <-> "OE2"
    Residue "A ARG  166": "NH1" <-> "NH2"
    Residue "A GLU  184": "OE1" <-> "OE2"
    Residue "A ARG  198": "NH1" <-> "NH2"
    Residue "A GLU  210": "OE1" <-> "OE2"
    Residue "A ARG  219": "NH1" <-> "NH2"
    Residue "A ARG  247": "NH1" <-> "NH2"
    Residue "A ARG  277": "NH1" <-> "NH2"
    Residue "A ARG  280": "NH1" <-> "NH2"
    Residue "A ARG  312": "NH1" <-> "NH2"
    Residue "A GLU  339": "OE1" <-> "OE2"
    Residue "A ARG  353": "NH1" <-> "NH2"
    Residue "A ARG  382": "NH1" <-> "NH2"
    Residue "A ARG  386": "NH1" <-> "NH2"
    Residue "A ARG  437": "NH1" <-> "NH2"
    Residue "A ARG  467": "NH1" <-> "NH2"
    Residue "A ARG  471": "NH1" <-> "NH2"
    Residue "A ARG  518": "NH1" <-> "NH2"
    Residue "A ARG  521": "NH1" <-> "NH2"
    Residue "A ARG  524": "NH1" <-> "NH2"
    Residue "A ARG  551": "NH1" <-> "NH2"
    Residue "A ARG  563": "NH1" <-> "NH2"
    Residue "A ARG  575": "NH1" <-> "NH2"
    Residue "A ARG  645": "NH1" <-> "NH2"
    Residue "A GLU  667": "OE1" <-> "OE2"
    Residue "A GLU  718": "OE1" <-> "OE2"
    Residue "A ARG  729": "NH1" <-> "NH2"
    Residue "A GLU  768": "OE1" <-> "OE2"
    Residue "A GLU  800": "OE1" <-> "OE2"
    Residue "A TYR  816": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  878": "OE1" <-> "OE2"
    Residue "A ARG  890": "NH1" <-> "NH2"
    Residue "A GLU  896": "OE1" <-> "OE2"
    Residue "A ARG  925": "NH1" <-> "NH2"
    Residue "A ARG  960": "NH1" <-> "NH2"
    Residue "A GLU  971": "OE1" <-> "OE2"
    Residue "A ARG 1080": "NH1" <-> "NH2"
    Residue "A ARG 1104": "NH1" <-> "NH2"
    Residue "A GLU 1119": "OE1" <-> "OE2"
    Residue "A ARG 1147": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9284
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1170, 9284
          Classifications: {'peptide': 1170}
          Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1127}
  Time building chain proxies: 5.18, per 1000 atoms: 0.56
  Number of scatterers: 9284
  At special positions: 0
  Unit cell: (92.394, 98.766, 210.276, 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    1800      8.00
     N    1629      7.00
     C    5816      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  - 3.50
        Amino acid           : False - 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: 3.44
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 9 sheets defined
      35.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 53
    Processing helix  chain 'A' and resid 58 through 74
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 306 through 338
      removed outlier: 3.910A  pdb=" N   HIS A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 372
      removed outlier: 3.806A  pdb=" N   ARG A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 652 through 658
    Processing helix  chain 'A' and resid 682 through 688
      removed outlier: 3.688A  pdb=" N   ASN A 688 " --> pdb=" O   TYR A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 754
    Processing helix  chain 'A' and resid 756 through 772
      removed outlier: 4.306A  pdb=" N   GLY A 770 " --> pdb=" O   SER A 766 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ARG A 771 " --> pdb=" O   GLN A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 777
      removed outlier: 3.627A  pdb=" N   LEU A 777 " --> pdb=" O   ASP A 774 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 774 through 777'
    Processing helix  chain 'A' and resid 778 through 796
      removed outlier: 3.611A  pdb=" N   SER A 796 " --> pdb=" O   MET A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 815
      removed outlier: 3.690A  pdb=" N   ILE A 804 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 835
    Processing helix  chain 'A' and resid 835 through 850
      removed outlier: 3.578A  pdb=" N   THR A 839 " --> pdb=" O   ALA A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 861
      removed outlier: 4.090A  pdb=" N   GLY A 861 " --> pdb=" O   THR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 885
    Processing helix  chain 'A' and resid 887 through 891
    Processing helix  chain 'A' and resid 897 through 901
    Processing helix  chain 'A' and resid 904 through 909
    Processing helix  chain 'A' and resid 909 through 923
      removed outlier: 3.606A  pdb=" N   PHE A 922 " --> pdb=" O   MET A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 938
      removed outlier: 3.873A  pdb=" N   ARG A 938 " --> pdb=" O   ASP A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 994
    Processing helix  chain 'A' and resid 1036 through 1040
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing helix  chain 'A' and resid 1094 through 1107
      removed outlier: 3.528A  pdb=" N   VAL A1106 " --> pdb=" O   ILE A1102 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP A1107 " --> pdb=" O   SER A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1136
      removed outlier: 3.593A  pdb=" N   LEU A1133 " --> pdb=" O   MET A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1146
    Processing helix  chain 'A' and resid 1148 through 1161
      removed outlier: 4.119A  pdb=" N   PHE A1152 " --> pdb=" O   ASN A1148 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   VAL A1153 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1194
      removed outlier: 4.322A  pdb=" N   ALA A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.949A  pdb=" N   ASN A 105 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A 106 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   GLU A 231 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LEU A 263 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU A 233 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 181
      removed outlier: 6.455A  pdb=" N   ASP A 155 " --> pdb=" O   TYR A 149 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   TYR A 149 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLU A 157 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLN A 124 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ARG A 125 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ILE A 284 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   PHE A 127 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214
      removed outlier: 4.133A  pdb=" N   ASN A1053 " --> pdb=" O   ILE A1062 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ILE A1062 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A1063 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ARG A1065 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 214
      removed outlier: 6.731A  pdb=" N   SER A1016 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 384
      removed outlier: 4.160A  pdb=" N   LEU A 379 " --> pdb=" O   TYR A 740 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 736 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE A 394 " --> pdb=" O   LEU A 726 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE A 728 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLY A 392 " --> pdb=" O   PHE A 728 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 730 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   GLY A 732 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASP A 388 " --> pdb=" O   GLY A 732 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 384
      removed outlier: 4.160A  pdb=" N   LEU A 379 " --> pdb=" O   TYR A 740 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 736 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A 729 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   GLU A 567 " --> pdb=" O   ARG A 729 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   HIS A 731 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   SER A 565 " --> pdb=" O   HIS A 731 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASN A 733 " --> pdb=" O   ARG A 563 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ARG A 737 " --> pdb=" O   ASP A 559 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   ASP A 559 " --> pdb=" O   ARG A 737 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408
      removed outlier: 3.613A  pdb=" N   TYR A 407 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 676 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A 441 " --> pdb=" O   VAL A 678 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 451 through 453
      removed outlier: 3.819A  pdb=" N   PHE A 468 " --> pdb=" O   HIS A 452 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG A 467 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   GLU A 545 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   SER A 469 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   VAL A 543 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 545 " --> pdb=" O   ILE A 602 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ILE A 602 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   LEU A 547 " --> pdb=" O   CYS A 600 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   CYS A 600 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   GLY A 549 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   LEU A 598 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 864 through 865
      removed outlier: 6.633A  pdb=" N   ASN A 864 " --> pdb=" O   GLU A1119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    404 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.42

  Time building geometry restraints manager: 3.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2732
        1.33 -     1.45: 1440
        1.45 -     1.57: 5209
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9455
  Sorted by residual:
  bond pdb=" CB  ASN A1030 "
       pdb=" CG  ASN A1030 "
    ideal  model  delta    sigma   weight residual
    1.516  1.472  0.044 2.50e-02 1.60e+03 3.11e+00
  bond pdb=" C   GLU A 679 "
       pdb=" N   LEU A 680 "
    ideal  model  delta    sigma   weight residual
    1.325  1.345 -0.020 1.25e-02 6.40e+03 2.67e+00
  bond pdb=" CG  GLN A1179 "
       pdb=" CD  GLN A1179 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.42e+00
  bond pdb=" CB  ASP A 182 "
       pdb=" CG  ASP A 182 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.38e+00
  bond pdb=" CB  ASP A 756 "
       pdb=" CG  ASP A 756 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.34e+00
  ... (remaining 9450 not shown)

  Histogram of bond angle deviations from ideal:
       97.44 -   104.78: 138
      104.78 -   112.13: 4725
      112.13 -   119.47: 3115
      119.47 -   126.81: 4764
      126.81 -   134.16: 86
  Bond angle restraints: 12828
  Sorted by residual:
  angle pdb=" N   GLY A 815 "
        pdb=" CA  GLY A 815 "
        pdb=" C   GLY A 815 "
      ideal   model   delta    sigma   weight residual
     114.92  120.28   -5.36 1.30e+00 5.92e-01 1.70e+01
  angle pdb=" CA  LEU A 777 "
        pdb=" C   LEU A 777 "
        pdb=" N   ASN A 778 "
      ideal   model   delta    sigma   weight residual
     118.27  112.71    5.56 1.59e+00 3.96e-01 1.22e+01
  angle pdb=" C   LEU A 240 "
        pdb=" N   HIS A 241 "
        pdb=" CA  HIS A 241 "
      ideal   model   delta    sigma   weight residual
     122.21  117.99    4.22 1.48e+00 4.57e-01 8.11e+00
  angle pdb=" N   VAL A 532 "
        pdb=" CA  VAL A 532 "
        pdb=" C   VAL A 532 "
      ideal   model   delta    sigma   weight residual
     107.71  111.90   -4.19 1.58e+00 4.01e-01 7.02e+00
  angle pdb=" N   ASP A 629 "
        pdb=" CA  ASP A 629 "
        pdb=" C   ASP A 629 "
      ideal   model   delta    sigma   weight residual
     111.36  114.08   -2.72 1.09e+00 8.42e-01 6.24e+00
  ... (remaining 12823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 5139
       16.96 -    33.91: 489
       33.91 -    50.86: 77
       50.86 -    67.82: 18
       67.82 -    84.77: 7
  Dihedral angle restraints: 5730
    sinusoidal: 2307
      harmonic: 3423
  Sorted by residual:
  dihedral pdb=" CA  ILE A 730 "
           pdb=" C   ILE A 730 "
           pdb=" N   HIS A 731 "
           pdb=" CA  HIS A 731 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.63   23.37     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  GLN A 755 "
           pdb=" C   GLN A 755 "
           pdb=" N   ASP A 756 "
           pdb=" CA  ASP A 756 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.28  -20.72     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  HIS A 136 "
           pdb=" C   HIS A 136 "
           pdb=" N   PHE A 137 "
           pdb=" CA  PHE A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.34  -19.66     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 5727 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 831
       0.040 -    0.081: 448
       0.081 -    0.121: 151
       0.121 -    0.162: 32
       0.162 -    0.202: 2
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CB  THR A1007 "
            pdb=" CA  THR A1007 "
            pdb=" OG1 THR A1007 "
            pdb=" CG2 THR A1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CG  LEU A 240 "
            pdb=" CB  LEU A 240 "
            pdb=" CD1 LEU A 240 "
            pdb=" CD2 LEU A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.76e-01
  chirality pdb=" CB  ILE A1063 "
            pdb=" CA  ILE A1063 "
            pdb=" CG1 ILE A1063 "
            pdb=" CG2 ILE A1063 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1461 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 952 "   -0.053 5.00e-02 4.00e+02   8.08e-02 1.04e+01
        pdb=" N   PRO A 953 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 953 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 953 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 234 "   -0.011 2.00e-02 2.50e+03   1.26e-02 3.19e+00
        pdb=" CG  TYR A 234 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 234 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 234 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 234 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 234 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 234 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 234 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 600 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A 601 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 601 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 601 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 280
        2.70 -     3.25: 8660
        3.25 -     3.80: 13899
        3.80 -     4.35: 17952
        4.35 -     4.90: 30950
  Nonbonded interactions: 71741
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 176 "
            pdb=" OG  SER A 237 "
     model   vdw
     2.147 2.440
  nonbonded pdb=" O   SER A 614 "
            pdb=" NH2 ARG A 698 "
     model   vdw
     2.207 2.520
  nonbonded pdb=" O   ILE A 546 "
            pdb=" OG1 THR A 599 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" NE2 GLN A  94 "
            pdb=" O   LEU A 276 "
     model   vdw
     2.249 2.520
  nonbonded pdb=" O   ARG A 721 "
            pdb=" N   THR A 725 "
     model   vdw
     2.270 2.520
  ... (remaining 71736 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  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:          7.190
  Check model and map are aligned:         0.120
  Set scattering table:                    0.090
  Process input model:                     27.460
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
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      :  0.009   0.057   9455  Z= 0.577
  Angle     :  0.800   7.926  12828  Z= 0.470
  Chirality :  0.053   0.202   1464
  Planarity :  0.005   0.081   1674
  Dihedral  : 13.811  84.774   3522
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -1.29 (0.22), residues: 1168
  helix:  0.45 (0.26), residues: 373
  sheet: -0.68 (0.32), residues: 241
  loop : -1.87 (0.22), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1099 
 HIS   0.007   0.002   HIS A 317 
 PHE   0.027   0.003   PHE A1140 
 TYR   0.031   0.003   TYR A 234 
 ARG   0.014   0.001   ARG A 219 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8279 (t0) cc_final: 0.7943 (t0)
REVERT: A  763 ASP cc_start: 0.7673 (m-30) cc_final: 0.6880 (m-30)
REVERT: A  768 GLU cc_start: 0.8162 (tp30) cc_final: 0.7191 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2843
  time to fit residues: 39.2199
Evaluate side-chains
  94 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0010
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
A 907 HIS
A 924 ASN
A 927 ASN
** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1167 ASN
A1179 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9455  Z= 0.145
  Angle     :  0.489   5.877  12828  Z= 0.266
  Chirality :  0.043   0.145   1464
  Planarity :  0.004   0.063   1674
  Dihedral  :  4.739  17.395   1298
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.91 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.33 (0.24), residues: 1168
  helix:  1.66 (0.27), residues: 383
  sheet: -0.52 (0.33), residues: 229
  loop : -1.47 (0.23), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 945 
 PHE   0.013   0.001   PHE A1003 
 TYR   0.015   0.001   TYR A1050 
 ARG   0.004   0.000   ARG A 381 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ASP cc_start: 0.7993 (t0) cc_final: 0.7720 (t0)
REVERT: A  763 ASP cc_start: 0.7565 (m-30) cc_final: 0.6994 (m-30)
REVERT: A  872 SER cc_start: 0.8896 (t) cc_final: 0.8647 (p)
  outliers start: 3
  outliers final: 3
  residues processed: 111
  average time/residue: 0.2413
  time to fit residues: 36.7156
Evaluate side-chains
  103 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  934 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 88 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 106 optimal weight:    6.9990
   chunk 114 optimal weight:    7.9990
   chunk 94 optimal weight:    0.3980
   chunk 105 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
A 864 ASN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 ASN
A1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9455  Z= 0.178
  Angle     :  0.474   5.769  12828  Z= 0.255
  Chirality :  0.043   0.138   1464
  Planarity :  0.004   0.058   1674
  Dihedral  :  4.449  16.424   1298
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  6.93 %
    Favored  : 92.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.01 (0.24), residues: 1168
  helix:  1.95 (0.27), residues: 388
  sheet: -0.03 (0.33), residues: 220
  loop : -1.44 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.015   0.001   PHE A1003 
 TYR   0.014   0.001   TYR A 234 
 ARG   0.004   0.000   ARG A 219 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ASP cc_start: 0.7933 (t0) cc_final: 0.7685 (t0)
REVERT: A  207 ASP cc_start: 0.6858 (t0) cc_final: 0.6494 (t70)
REVERT: A  763 ASP cc_start: 0.7570 (m-30) cc_final: 0.6888 (m-30)
REVERT: A  872 SER cc_start: 0.8995 (t) cc_final: 0.8691 (p)
  outliers start: 11
  outliers final: 5
  residues processed: 112
  average time/residue: 0.2506
  time to fit residues: 38.7424
Evaluate side-chains
  108 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  966 ASP
Chi-restraints excluded: chain A residue 1117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 71 optimal weight:    0.6980
   chunk 106 optimal weight:    0.1980
   chunk 113 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 94 optimal weight:    9.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
A1040 ASN
A1053 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9455  Z= 0.138
  Angle     :  0.434   5.634  12828  Z= 0.233
  Chirality :  0.042   0.135   1464
  Planarity :  0.003   0.054   1674
  Dihedral  :  4.156  14.287   1298
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.18 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.34 (0.24), residues: 1168
  helix:  2.26 (0.27), residues: 387
  sheet:  0.16 (0.34), residues: 221
  loop : -1.28 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1099 
 HIS   0.010   0.001   HIS A 307 
 PHE   0.014   0.001   PHE A1003 
 TYR   0.014   0.001   TYR A1050 
 ARG   0.002   0.000   ARG A 219 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ASP cc_start: 0.7792 (t0) cc_final: 0.7542 (t0)
REVERT: A  207 ASP cc_start: 0.6744 (t0) cc_final: 0.6390 (t70)
REVERT: A  872 SER cc_start: 0.8894 (t) cc_final: 0.8660 (p)
  outliers start: 14
  outliers final: 6
  residues processed: 117
  average time/residue: 0.2318
  time to fit residues: 37.5453
Evaluate side-chains
  111 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue 1040 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0370
   chunk 96 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9455  Z= 0.120
  Angle     :  0.428   7.052  12828  Z= 0.228
  Chirality :  0.041   0.133   1464
  Planarity :  0.003   0.052   1674
  Dihedral  :  3.998  13.544   1298
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.72 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.53 (0.25), residues: 1168
  helix:  2.40 (0.27), residues: 388
  sheet:  0.08 (0.33), residues: 234
  loop : -1.08 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1099 
 HIS   0.003   0.000   HIS A 317 
 PHE   0.013   0.001   PHE A1003 
 TYR   0.012   0.001   TYR A1050 
 ARG   0.005   0.000   ARG A 219 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A  872 SER cc_start: 0.8863 (t) cc_final: 0.8638 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2413
  time to fit residues: 37.6074
Evaluate side-chains
  108 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  609 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 754 HIS
A 767 GLN
A 924 ASN
A 927 ASN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   9455  Z= 0.461
  Angle     :  0.610   7.749  12828  Z= 0.324
  Chirality :  0.048   0.146   1464
  Planarity :  0.005   0.053   1674
  Dihedral  :  4.784  17.741   1298
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.11 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.02 (0.24), residues: 1168
  helix:  1.75 (0.27), residues: 380
  sheet: -0.08 (0.32), residues: 239
  loop : -1.22 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1099 
 HIS   0.009   0.002   HIS A 317 
 PHE   0.021   0.002   PHE A1003 
 TYR   0.020   0.002   TYR A 234 
 ARG   0.004   0.001   ARG A 129 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8211 (mt-10)
REVERT: A  763 ASP cc_start: 0.7686 (m-30) cc_final: 0.6972 (m-30)
REVERT: A  768 GLU cc_start: 0.8024 (tp30) cc_final: 0.7075 (mt-10)
REVERT: A  866 SER cc_start: 0.8769 (t) cc_final: 0.8538 (m)
REVERT: A  872 SER cc_start: 0.9197 (t) cc_final: 0.8924 (t)
  outliers start: 20
  outliers final: 10
  residues processed: 114
  average time/residue: 0.2538
  time to fit residues: 39.3815
Evaluate side-chains
  113 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 112 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 68 optimal weight:    0.1980
   chunk 52 optimal weight:    0.3980
   chunk 69 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
A 864 ASN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9455  Z= 0.162
  Angle     :  0.459   6.169  12828  Z= 0.245
  Chirality :  0.042   0.137   1464
  Planarity :  0.003   0.050   1674
  Dihedral  :  4.286  14.168   1298
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 10.88 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.44 (0.24), residues: 1168
  helix:  2.32 (0.27), residues: 379
  sheet: -0.08 (0.33), residues: 231
  loop : -1.00 (0.24), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.014   0.001   PHE A1003 
 TYR   0.015   0.001   TYR A1050 
 ARG   0.002   0.000   ARG A 341 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ASP cc_start: 0.8187 (t0) cc_final: 0.7871 (t0)
REVERT: A  763 ASP cc_start: 0.7604 (m-30) cc_final: 0.6913 (m-30)
REVERT: A  768 GLU cc_start: 0.8112 (tp30) cc_final: 0.7183 (mt-10)
REVERT: A  872 SER cc_start: 0.8947 (t) cc_final: 0.8646 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 113
  average time/residue: 0.2492
  time to fit residues: 38.4586
Evaluate side-chains
  112 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0270
   chunk 76 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9455  Z= 0.114
  Angle     :  0.421   5.756  12828  Z= 0.225
  Chirality :  0.042   0.325   1464
  Planarity :  0.003   0.049   1674
  Dihedral  :  3.926  14.043   1298
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.16 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.77 (0.25), residues: 1168
  helix:  2.68 (0.27), residues: 379
  sheet: -0.12 (0.33), residues: 236
  loop : -0.77 (0.25), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1099 
 HIS   0.003   0.000   HIS A 317 
 PHE   0.013   0.001   PHE A1003 
 TYR   0.013   0.001   TYR A1050 
 ARG   0.003   0.000   ARG A 720 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 ASP cc_start: 0.7970 (t0) cc_final: 0.7758 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 115
  average time/residue: 0.2432
  time to fit residues: 38.4085
Evaluate side-chains
  109 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue 1058 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9455  Z= 0.149
  Angle     :  0.436   6.026  12828  Z= 0.232
  Chirality :  0.042   0.241   1464
  Planarity :  0.003   0.050   1674
  Dihedral  :  3.935  13.409   1298
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.65 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.82 (0.25), residues: 1168
  helix:  2.68 (0.27), residues: 379
  sheet: -0.09 (0.32), residues: 248
  loop : -0.70 (0.25), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.014   0.001   PHE A1003 
 TYR   0.012   0.001   TYR A1050 
 ARG   0.002   0.000   ARG A 341 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A  763 ASP cc_start: 0.7524 (m-30) cc_final: 0.6904 (m-30)
  outliers start: 6
  outliers final: 5
  residues processed: 110
  average time/residue: 0.2543
  time to fit residues: 38.1026
Evaluate side-chains
  109 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0060
   chunk 52 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 116 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0770
   chunk 56 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.5354

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9455  Z= 0.110
  Angle     :  0.417   5.650  12828  Z= 0.222
  Chirality :  0.041   0.249   1464
  Planarity :  0.003   0.049   1674
  Dihedral  :  3.781  14.753   1298
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 11.36 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.96 (0.25), residues: 1168
  helix:  2.80 (0.27), residues: 379
  sheet: -0.07 (0.33), residues: 240
  loop : -0.58 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1099 
 HIS   0.003   0.000   HIS A 317 
 PHE   0.013   0.001   PHE A 128 
 TYR   0.012   0.001   TYR A1050 
 ARG   0.002   0.000   ARG A 341 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 ASP cc_start: 0.7558 (t70) cc_final: 0.7285 (t70)
REVERT: A  768 GLU cc_start: 0.8138 (tp30) cc_final: 0.6972 (mt-10)
REVERT: A 1079 ASP cc_start: 0.7657 (m-30) cc_final: 0.7247 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 112
  average time/residue: 0.2575
  time to fit residues: 39.1313
Evaluate side-chains
  109 residues out of total 1039 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  438 ASN
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.188530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.130202 restraints weight = 10374.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.80
r_work: 0.3032 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9455  Z= 0.137
  Angle     :  0.431   5.946  12828  Z= 0.227
  Chirality :  0.042   0.241   1464
  Planarity :  0.003   0.049   1674
  Dihedral  :  3.797  13.227   1298
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.45 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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:  0.96 (0.25), residues: 1168
  helix:  2.73 (0.27), residues: 379
  sheet: -0.01 (0.32), residues: 250
  loop : -0.56 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.013   0.001   PHE A1003 
 TYR   0.012   0.001   TYR A1050 
 ARG   0.002   0.000   ARG A 437 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2179.23 seconds
wall clock time: 39 minutes 43.33 seconds (2383.33 seconds total)