Starting phenix.real_space_refine
on Thu Jul 31 08:44:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pzr_13736/07_2025/7pzr_13736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pzr_13736/07_2025/7pzr_13736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pzr_13736/07_2025/7pzr_13736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pzr_13736/07_2025/7pzr_13736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pzr_13736/07_2025/7pzr_13736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pzr_13736/07_2025/7pzr_13736.cif"
  }
  resolution = 3.0
  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=  -0.007 sd=   0.123
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7365 atoms to isotropic.
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      49      5.16       5
     C    4712      2.51       5
     N    1336      2.21       5
     O    1307      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7404
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7404
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 935, 7362
          Classifications: {'peptide': 935}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 61, 'TRANS': 873}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 45
      Conformer: "B"
        Number of residues, atoms: 935, 7362
          Classifications: {'peptide': 935}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 61, 'TRANS': 873}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 45
          bond proxies already assigned to first conformer: 7485
  Time building chain proxies: 9.04, per 1000 atoms: 1.22
  Number of scatterers: 7404
  At special positions: 0
  Unit cell: (81.81, 93.93, 103.02, 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      49     16.00
     O    1307      8.00
     N    1336      7.00
     C    4712      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: 1.83
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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:  1792

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      68.8% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 220 through 237
    Processing helix  chain 'A' and resid 238 through 252
    Processing helix  chain 'A' and resid 252 through 259
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 276 through 291
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 312 through 326
    Processing helix  chain 'A' and resid 329 through 337
    Processing helix  chain 'A' and resid 340 through 354
    Processing helix  chain 'A' and resid 371 through 376
      removed outlier: 4.116A  pdb=" N   ASP A 376 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 410
    Processing helix  chain 'A' and resid 424 through 463
    Processing helix  chain 'A' and resid 467 through 474
      removed outlier: 4.030A  pdb=" N   LEU A 474 " --> pdb=" O   PHE A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 490
    Processing helix  chain 'A' and resid 497 through 521
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 3.810A  pdb=" N   LEU A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 557
    Processing helix  chain 'A' and resid 568 through 587
    Processing helix  chain 'A' and resid 624 through 635
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 688 through 705
      removed outlier: 3.918A  pdb=" N   ALA A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
    Processing helix  chain 'A' and resid 771 through 789
    Processing helix  chain 'A' and resid 818 through 824
    Processing helix  chain 'A' and resid 836 through 850
    Processing helix  chain 'A' and resid 856 through 867
    Processing helix  chain 'A' and resid 867 through 877
    Processing helix  chain 'A' and resid 883 through 888
    Processing helix  chain 'A' and resid 890 through 907
    Processing helix  chain 'A' and resid 925 through 936
    Processing helix  chain 'A' and resid 937 through 944
    Processing helix  chain 'A' and resid 954 through 973
    Processing helix  chain 'A' and resid 976 through 982
    Processing helix  chain 'A' and resid 986 through 999
    Processing helix  chain 'A' and resid 1003 through 1017
      removed outlier: 4.424A  pdb=" N   ARG A1007 " --> pdb=" O   ARG A1003 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU A1017 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1044
    Processing helix  chain 'A' and resid 1044 through 1065
    Processing helix  chain 'A' and resid 1111 through 1143
      Proline residue:  A1120  - end of helix
    Processing helix  chain 'A' and resid 1156 through 1177
      removed outlier: 4.318A  pdb=" N   SER A1161 " --> pdb=" O   ALA A1157 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   VAL A1162 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A1172 " --> pdb=" O   ARG A1168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1192
    Processing helix  chain 'A' and resid 1201 through 1210
    Processing helix  chain 'A' and resid 1220 through 1225
      removed outlier: 3.664A  pdb=" N   ARG A1224 " --> pdb=" O   GLU A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1229
      removed outlier: 4.093A  pdb=" N   PHE A1229 " --> pdb=" O   THR A1226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1226 through 1229'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415
    Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496
    Processing sheet with id=AA3, first strand: chain 'A' and resid 794 through 795
    Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 800
    Processing sheet with id=AA5, first strand: chain 'A' and resid 919 through 921
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1069 through 1071

    484 hydrogen bonds defined for protein.
    1434 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: 2.42

  Time building geometry restraints manager: 2.16 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: 1599
        1.33 -     1.45: 1602
        1.45 -     1.57: 4309
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 7585
  Sorted by residual:
  bond pdb=" CB  ILE A1124 "
       pdb=" CG1 ILE A1124 "
    ideal  model  delta    sigma   weight residual
    1.530  1.498  0.032 2.00e-02 2.50e+03 2.59e+00
  bond pdb=" CG1 ILE A1124 "
       pdb=" CD1 ILE A1124 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.21e+00
  bond pdb=" CB  ASN A 799 "
       pdb=" CG  ASN A 799 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.18e+00
  bond pdb=" CG  LEU A 490 "
       pdb=" CD2 LEU A 490 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.48e+00
  bond pdb=" CB  VAL A1149 "
       pdb=" CG2 VAL A1149 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.27e+00
  ... (remaining 7580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 9972
        1.77 -     3.53: 290
        3.53 -     5.30: 34
        5.30 -     7.06: 8
        7.06 -     8.83: 2
  Bond angle restraints: 10306
  Sorted by residual:
  angle pdb=" N   PHE A1229 "
        pdb=" CA  PHE A1229 "
        pdb=" CB  PHE A1229 "
      ideal   model   delta    sigma   weight residual
     110.68  119.51   -8.83 1.68e+00 3.54e-01 2.76e+01
  angle pdb=" N   ARG A 273 "
        pdb=" CA  ARG A 273 "
        pdb=" C   ARG A 273 "
      ideal   model   delta    sigma   weight residual
     113.97  109.29    4.68 1.28e+00 6.10e-01 1.34e+01
  angle pdb=" C   ARG A 273 "
        pdb=" N   GLN A 274 "
        pdb=" CA  GLN A 274 "
      ideal   model   delta    sigma   weight residual
     121.52  127.19   -5.67 1.84e+00 2.95e-01 9.51e+00
  angle pdb=" C   GLY A 923 "
        pdb=" N   SER A 924 "
        pdb=" CA  SER A 924 "
      ideal   model   delta    sigma   weight residual
     121.54  127.35   -5.81 1.91e+00 2.74e-01 9.25e+00
  angle pdb=" N   GLY A 521 "
        pdb=" CA  GLY A 521 "
        pdb=" C   GLY A 521 "
      ideal   model   delta    sigma   weight residual
     115.64  111.30    4.34 1.46e+00 4.69e-01 8.83e+00
  ... (remaining 10301 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4251
       17.83 -    35.66: 315
       35.66 -    53.48: 52
       53.48 -    71.31: 12
       71.31 -    89.14: 3
  Dihedral angle restraints: 4633
    sinusoidal: 1873
      harmonic: 2760
  Sorted by residual:
  dihedral pdb=" N   PHE A1229 "
           pdb=" C   PHE A1229 "
           pdb=" CA  PHE A1229 "
           pdb=" CB  PHE A1229 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.61   -7.81     0      2.50e+00 1.60e-01 9.75e+00
  dihedral pdb=" CB AMET A 671 "
           pdb=" CG AMET A 671 "
           pdb=" SD AMET A 671 "
           pdb=" CE AMET A 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.68  -59.68     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ARG A 967 "
           pdb=" CB  ARG A 967 "
           pdb=" CG  ARG A 967 "
           pdb=" CD  ARG A 967 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -130.70  -49.30     3      1.50e+01 4.44e-03 8.76e+00
  ... (remaining 4630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 881
       0.043 -    0.086: 187
       0.086 -    0.129: 64
       0.129 -    0.172: 11
       0.172 -    0.216: 5
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" CB  VAL A1149 "
            pdb=" CA  VAL A1149 "
            pdb=" CG1 VAL A1149 "
            pdb=" CG2 VAL A1149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CG  LEU A 473 "
            pdb=" CB  LEU A 473 "
            pdb=" CD1 LEU A 473 "
            pdb=" CD2 LEU A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.94e-01
  chirality pdb=" CB  VAL A 867 "
            pdb=" CA  VAL A 867 "
            pdb=" CG1 VAL A 867 "
            pdb=" CG2 VAL A 867 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.67e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1337
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1229 "    0.049 2.00e-02 2.50e+03   4.54e-02 3.61e+01
        pdb=" CG  PHE A1229 "   -0.105 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1229 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1229 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1229 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1229 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1229 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 512 "   -0.030 2.00e-02 2.50e+03   2.78e-02 1.16e+01
        pdb=" CG  HIS A 512 "    0.059 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 512 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 512 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 512 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 512 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A1167 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.81e+00
        pdb=" C   CYS A1167 "    0.054 2.00e-02 2.50e+03
        pdb=" O   CYS A1167 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A1168 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1334 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 25
        2.63 -     3.20: 6794
        3.20 -     3.76: 12635
        3.76 -     4.33: 17269
        4.33 -     4.90: 27323
  Nonbonded interactions: 64046
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 900 "
            pdb=" OH  TYR A 913 "
     model   vdw
     2.062 3.040
  nonbonded pdb=" O   VAL A 963 "
            pdb=" NE2 GLN A1035 "
     model   vdw
     2.156 3.120
  nonbonded pdb=" OD1 ASN A 528 "
            pdb=" NH2 ARG A 531 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" ND2 ASN A 369 "
            pdb=" O   THR A 690 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   LEU A 235 "
            pdb=" NH2 ARG A 516 "
     model   vdw
     2.295 3.120
  ... (remaining 64041 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=0.50 max=1.00 mean=0.99
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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     26.540
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7585  Z= 0.177
  Angle     :  0.706   8.828  10306  Z= 0.417
  Chirality :  0.043   0.216   1148
  Planarity :  0.005   0.075   1337
  Dihedral  : 12.708  89.141   2841
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.84 (0.27), residues: 930
  helix:  3.32 (0.20), residues: 626
  sheet:  0.96 (1.13), residues: 23
  loop :  0.89 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 892 
 HIS   0.025   0.003   HIS A 512 
 PHE   0.105   0.003   PHE A1229 
 TYR   0.043   0.002   TYR A 610 
 ARG   0.016   0.001   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12859 (  484)
  hydrogen bonds       : angle       5.12755 ( 1434)
  covalent geometry    : bond        0.00368 ( 7585)
  covalent geometry    : angle       0.70621 (10306)

*********************** 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
  237 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  395 THR cc_start: 0.8442 (m) cc_final: 0.8148 (p)
REVERT: A  482 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttm)
REVERT: A  495 GLU cc_start: 0.8442 (tp30) cc_final: 0.8220 (tm-30)
REVERT: A  988 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6980 (mptt)
REVERT: A  992 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7195 (tm-30)
REVERT: A 1038 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7234 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 1.5086
  time to fit residues: 376.0710
Evaluate side-chains
  126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 252 GLN
A 390 HIS
** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.145095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.110893 restraints weight = 41998.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 5.94
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3869 r_free = 0.3869    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7585  Z= 0.183
  Angle     :  0.747  10.817  10306  Z= 0.373
  Chirality :  0.039   0.141   1148
  Planarity :  0.006   0.071   1337
  Dihedral  :  4.247  40.779   1035
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.60 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.26), residues: 930
  helix:  2.41 (0.20), residues: 637
  sheet:  0.30 (0.86), residues: 33
  loop :  0.60 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A1154 
 HIS   0.011   0.002   HIS A 512 
 PHE   0.048   0.003   PHE A 802 
 TYR   0.018   0.002   TYR A1031 
 ARG   0.009   0.001   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05349 (  484)
  hydrogen bonds       : angle       4.53968 ( 1434)
  covalent geometry    : bond        0.00416 ( 7585)
  covalent geometry    : angle       0.74719 (10306)

*********************** 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
  158 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 GLN cc_start: 0.9320 (tp40) cc_final: 0.9013 (tm-30)
REVERT: A  286 MET cc_start: 0.7612 (mmp) cc_final: 0.7393 (mmp)
REVERT: A  395 THR cc_start: 0.8568 (m) cc_final: 0.8364 (p)
REVERT: A  425 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8536 (pptt)
REVERT: A  495 GLU cc_start: 0.8865 (tp30) cc_final: 0.8222 (tm-30)
REVERT: A  772 MET cc_start: 0.7576 (tmm) cc_final: 0.7097 (tmm)
REVERT: A  972 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7906 (mp10)
REVERT: A  975 MET cc_start: 0.7868 (mmm) cc_final: 0.6958 (ttm)
REVERT: A  992 GLN cc_start: 0.7514 (tp-100) cc_final: 0.6991 (tm-30)
REVERT: A 1062 SER cc_start: 0.8925 (m) cc_final: 0.8492 (p)
  outliers start: 26
  outliers final: 8
  residues processed: 148
  average time/residue: 1.2680
  time to fit residues: 199.9643
Evaluate side-chains
  106 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  632 GLU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  666 SER
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  972 GLN
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1230 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 GLN
A 681 GLN
A 815 HIS
A1009 GLN
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.143589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.108660 restraints weight = 47487.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 6.28
r_work: 0.3629 rms_B_bonded: 6.06 restraints_weight: 2.0000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7585  Z= 0.156
  Angle     :  0.719  13.521  10306  Z= 0.350
  Chirality :  0.038   0.129   1148
  Planarity :  0.005   0.049   1337
  Dihedral  :  4.202  41.176   1035
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.28 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.27), residues: 930
  helix:  2.14 (0.20), residues: 627
  sheet:  0.06 (0.87), residues: 35
  loop :  0.57 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A1154 
 HIS   0.006   0.001   HIS A 624 
 PHE   0.033   0.003   PHE A 802 
 TYR   0.034   0.002   TYR A 468 
 ARG   0.014   0.001   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04674 (  484)
  hydrogen bonds       : angle       4.52991 ( 1434)
  covalent geometry    : bond        0.00359 ( 7585)
  covalent geometry    : angle       0.71944 (10306)

*********************** 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
  129 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 2.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7792 (ptm)
REVERT: A  268 MET cc_start: 0.8391 (mpt) cc_final: 0.8157 (mmm)
REVERT: A  321 GLU cc_start: 0.7925 (pt0) cc_final: 0.7627 (pp20)
REVERT: A  372 LYS cc_start: 0.7755 (pmtt) cc_final: 0.7283 (tptp)
REVERT: A  495 GLU cc_start: 0.8968 (tp30) cc_final: 0.8436 (tm-30)
REVERT: A  502 ARG cc_start: 0.8238 (mtt90) cc_final: 0.8024 (mmp80)
REVERT: A  868 MET cc_start: 0.7547 (tmm) cc_final: 0.6458 (tpp)
REVERT: A  975 MET cc_start: 0.7973 (mmm) cc_final: 0.7192 (ttm)
REVERT: A 1062 SER cc_start: 0.9065 (m) cc_final: 0.8589 (p)
  outliers start: 19
  outliers final: 6
  residues processed: 121
  average time/residue: 1.1412
  time to fit residues: 149.5448
Evaluate side-chains
  93 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  510 SER
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue 1019 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 92 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0770
   chunk 59 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   overall best weight:    1.1140

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.141776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.106941 restraints weight = 41024.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 5.85
r_work: 0.3607 rms_B_bonded: 5.76 restraints_weight: 2.0000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7585  Z= 0.152
  Angle     :  0.727  14.520  10306  Z= 0.343
  Chirality :  0.039   0.194   1148
  Planarity :  0.005   0.042   1337
  Dihedral  :  4.161  39.463   1035
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.79 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.27), residues: 930
  helix:  2.06 (0.20), residues: 627
  sheet:  0.19 (0.90), residues: 35
  loop :  0.55 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1154 
 HIS   0.005   0.001   HIS A 624 
 PHE   0.032   0.002   PHE A 465 
 TYR   0.027   0.002   TYR A 533 
 ARG   0.009   0.001   ARG A 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  484)
  hydrogen bonds       : angle       4.42460 ( 1434)
  covalent geometry    : bond        0.00349 ( 7585)
  covalent geometry    : angle       0.72748 (10306)

*********************** 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
  126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 MET cc_start: 0.8314 (mpt) cc_final: 0.7956 (mmm)
REVERT: A  321 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7670 (pp20)
REVERT: A  372 LYS cc_start: 0.7780 (pmtt) cc_final: 0.7338 (tptp)
REVERT: A  495 GLU cc_start: 0.9000 (tp30) cc_final: 0.8488 (tm-30)
REVERT: A  566 PRO cc_start: 0.8074 (Cg_endo) cc_final: 0.7838 (Cg_exo)
REVERT: A  772 MET cc_start: 0.7557 (tmm) cc_final: 0.7130 (tmm)
REVERT: A  868 MET cc_start: 0.7608 (tmm) cc_final: 0.6620 (tpp)
REVERT: A  975 MET cc_start: 0.8009 (mmm) cc_final: 0.7229 (ttt)
REVERT: A 1062 SER cc_start: 0.9115 (m) cc_final: 0.8639 (p)
  outliers start: 24
  outliers final: 13
  residues processed: 116
  average time/residue: 0.8821
  time to fit residues: 110.6267
Evaluate side-chains
  101 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  632 GLU
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0570
   chunk 15 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7102

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 953 GLN
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 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 = 0.4301 r_free = 0.4301 target = 0.141788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.107903 restraints weight = 38472.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 5.61
r_work: 0.3636 rms_B_bonded: 5.59 restraints_weight: 2.0000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7585  Z= 0.138
  Angle     :  0.724  15.322  10306  Z= 0.338
  Chirality :  0.039   0.326   1148
  Planarity :  0.005   0.042   1337
  Dihedral  :  4.135  40.709   1035
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.91 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.27), residues: 930
  helix:  1.99 (0.21), residues: 627
  sheet:  0.29 (0.88), residues: 35
  loop :  0.56 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1154 
 HIS   0.005   0.001   HIS A 624 
 PHE   0.033   0.002   PHE A 277 
 TYR   0.031   0.002   TYR A 533 
 ARG   0.007   0.001   ARG A 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  484)
  hydrogen bonds       : angle       4.35487 ( 1434)
  covalent geometry    : bond        0.00316 ( 7585)
  covalent geometry    : angle       0.72368 (10306)

*********************** 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
  128 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7667 (ptm)
REVERT: A  268 MET cc_start: 0.8320 (mpt) cc_final: 0.7929 (mmm)
REVERT: A  286 MET cc_start: 0.7602 (mmp) cc_final: 0.7396 (tpp)
REVERT: A  321 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7642 (pp20)
REVERT: A  372 LYS cc_start: 0.7792 (pmtt) cc_final: 0.7460 (tptp)
REVERT: A  482 MET cc_start: 0.8000 (ttm) cc_final: 0.7722 (ptt)
REVERT: A  495 GLU cc_start: 0.8948 (tp30) cc_final: 0.8443 (tm-30)
REVERT: A  533 TYR cc_start: 0.7803 (t80) cc_final: 0.7472 (t80)
REVERT: A  566 PRO cc_start: 0.8002 (Cg_endo) cc_final: 0.7782 (Cg_exo)
REVERT: A  772 MET cc_start: 0.7561 (tmm) cc_final: 0.7065 (tmm)
REVERT: A  778 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7791 (mp0)
REVERT: A  868 MET cc_start: 0.7541 (tmm) cc_final: 0.6657 (tpp)
REVERT: A  987 ARG cc_start: 0.6897 (ttt-90) cc_final: 0.6558 (ttm170)
REVERT: A  992 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7510 (tm-30)
REVERT: A 1062 SER cc_start: 0.9132 (m) cc_final: 0.8684 (p)
  outliers start: 28
  outliers final: 11
  residues processed: 118
  average time/residue: 0.9424
  time to fit residues: 119.9978
Evaluate side-chains
  107 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 70 optimal weight:    0.4980
   chunk 66 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0010
   chunk 18 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 921 GLN
** A1115 GLN ** 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 = 0.4310 r_free = 0.4310 target = 0.142523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.110319 restraints weight = 31111.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 5.15
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7585  Z= 0.132
  Angle     :  0.722  13.817  10306  Z= 0.335
  Chirality :  0.040   0.374   1148
  Planarity :  0.005   0.042   1337
  Dihedral  :  4.103  42.427   1035
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.94 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.27), residues: 930
  helix:  2.00 (0.21), residues: 627
  sheet:  0.23 (0.87), residues: 35
  loop :  0.55 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 567 
 HIS   0.004   0.001   HIS A 624 
 PHE   0.031   0.002   PHE A 465 
 TYR   0.025   0.002   TYR A 533 
 ARG   0.010   0.001   ARG A 976 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  484)
  hydrogen bonds       : angle       4.32368 ( 1434)
  covalent geometry    : bond        0.00302 ( 7585)
  covalent geometry    : angle       0.72221 (10306)

*********************** 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
  121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7810 (ptm)
REVERT: A  268 MET cc_start: 0.8326 (mpt) cc_final: 0.8036 (mmm)
REVERT: A  277 PHE cc_start: 0.7692 (t80) cc_final: 0.6883 (t80)
REVERT: A  280 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8773 (tp)
REVERT: A  321 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7669 (pp20)
REVERT: A  372 LYS cc_start: 0.7769 (pmtt) cc_final: 0.7495 (tptp)
REVERT: A  432 LYS cc_start: 0.9086 (ptmt) cc_final: 0.8881 (pttm)
REVERT: A  451 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8695 (mm-30)
REVERT: A  482 MET cc_start: 0.7864 (ttm) cc_final: 0.7575 (ptt)
REVERT: A  495 GLU cc_start: 0.8901 (tp30) cc_final: 0.8400 (tm-30)
REVERT: A  772 MET cc_start: 0.7635 (tmm) cc_final: 0.7203 (tmm)
REVERT: A  868 MET cc_start: 0.7066 (tmm) cc_final: 0.6402 (tpp)
REVERT: A  975 MET cc_start: 0.7711 (mmm) cc_final: 0.7041 (ttt)
REVERT: A  987 ARG cc_start: 0.6943 (ttt-90) cc_final: 0.6548 (ttm170)
REVERT: A  992 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7257 (tm-30)
REVERT: A 1062 SER cc_start: 0.8944 (m) cc_final: 0.8483 (p)
  outliers start: 19
  outliers final: 9
  residues processed: 114
  average time/residue: 0.9872
  time to fit residues: 120.8457
Evaluate side-chains
  111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 82 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.141489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.107519 restraints weight = 35663.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 5.35
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.5342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7585  Z= 0.140
  Angle     :  0.734  13.875  10306  Z= 0.340
  Chirality :  0.040   0.354   1148
  Planarity :  0.005   0.085   1337
  Dihedral  :  4.125  41.093   1035
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.07 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.27), residues: 930
  helix:  2.04 (0.21), residues: 620
  sheet:  0.13 (0.88), residues: 35
  loop :  0.49 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A 512 
 PHE   0.032   0.002   PHE A 465 
 TYR   0.014   0.001   TYR A1004 
 ARG   0.011   0.001   ARG A 976 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 (  484)
  hydrogen bonds       : angle       4.36384 ( 1434)
  covalent geometry    : bond        0.00323 ( 7585)
  covalent geometry    : angle       0.73395 (10306)

*********************** 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
  127 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7571 (ptm)
REVERT: A  268 MET cc_start: 0.8262 (mpt) cc_final: 0.7997 (mmm)
REVERT: A  280 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8758 (tp)
REVERT: A  321 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7726 (pp20)
REVERT: A  432 LYS cc_start: 0.9083 (ptmt) cc_final: 0.8883 (pttm)
REVERT: A  451 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: A  482 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7696 (ptt)
REVERT: A  495 GLU cc_start: 0.8995 (tp30) cc_final: 0.8335 (tm-30)
REVERT: A  772 MET cc_start: 0.7700 (tmm) cc_final: 0.7320 (tmm)
REVERT: A  868 MET cc_start: 0.7029 (tmm) cc_final: 0.6388 (tpp)
REVERT: A  975 MET cc_start: 0.7831 (mmm) cc_final: 0.6894 (ttt)
REVERT: A  992 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7228 (tm-30)
REVERT: A 1062 SER cc_start: 0.8981 (m) cc_final: 0.8528 (p)
REVERT: A 1219 LEU cc_start: 0.7878 (tp) cc_final: 0.7678 (mt)
  outliers start: 24
  outliers final: 11
  residues processed: 119
  average time/residue: 1.1383
  time to fit residues: 144.9817
Evaluate side-chains
  107 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.138409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.102757 restraints weight = 49260.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 6.31
r_work: 0.3544 rms_B_bonded: 5.99 restraints_weight: 2.0000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7585  Z= 0.176
  Angle     :  0.773  13.823  10306  Z= 0.365
  Chirality :  0.041   0.361   1148
  Planarity :  0.005   0.070   1337
  Dihedral  :  4.204  35.205   1035
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.08 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.27), residues: 930
  helix:  1.88 (0.21), residues: 620
  sheet:  0.13 (0.90), residues: 35
  loop :  0.39 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1154 
 HIS   0.005   0.001   HIS A 512 
 PHE   0.037   0.002   PHE A 465 
 TYR   0.012   0.001   TYR A1004 
 ARG   0.010   0.001   ARG A 976 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04391 (  484)
  hydrogen bonds       : angle       4.46047 ( 1434)
  covalent geometry    : bond        0.00415 ( 7585)
  covalent geometry    : angle       0.77290 (10306)

*********************** 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
  124 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7589 (ptm)
REVERT: A  268 MET cc_start: 0.8387 (mpt) cc_final: 0.8044 (mmm)
REVERT: A  280 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8616 (tp)
REVERT: A  297 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (mm)
REVERT: A  321 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7634 (pp20)
REVERT: A  441 TRP cc_start: 0.7909 (m-10) cc_final: 0.7381 (m-90)
REVERT: A  451 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8969 (mm-30)
REVERT: A  482 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7926 (ptt)
REVERT: A  495 GLU cc_start: 0.9097 (tp30) cc_final: 0.8593 (tm-30)
REVERT: A  560 GLU cc_start: 0.8239 (pm20) cc_final: 0.6941 (tp30)
REVERT: A  621 LEU cc_start: 0.9056 (mt) cc_final: 0.8839 (mt)
REVERT: A  772 MET cc_start: 0.7762 (tmm) cc_final: 0.7284 (tmm)
REVERT: A  805 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7618 (mtp85)
REVERT: A  868 MET cc_start: 0.7545 (tmm) cc_final: 0.6714 (tpp)
REVERT: A  972 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8011 (mp10)
REVERT: A  975 MET cc_start: 0.7990 (mmm) cc_final: 0.7085 (ttt)
REVERT: A  992 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7560 (tm-30)
REVERT: A 1042 GLU cc_start: 0.8629 (tp30) cc_final: 0.8366 (tm-30)
REVERT: A 1062 SER cc_start: 0.9106 (m) cc_final: 0.8662 (p)
REVERT: A 1219 LEU cc_start: 0.8307 (tp) cc_final: 0.7881 (mt)
  outliers start: 22
  outliers final: 13
  residues processed: 117
  average time/residue: 1.2522
  time to fit residues: 156.9815
Evaluate side-chains
  114 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  972 GLN
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 78 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   chunk 14 optimal weight:   20.0000
   chunk 30 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 43 optimal weight:    0.4980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 GLN
** A1115 GLN ** 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 = 0.4291 r_free = 0.4291 target = 0.140914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.106187 restraints weight = 39483.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 5.65
r_work: 0.3612 rms_B_bonded: 5.62 restraints_weight: 2.0000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7585  Z= 0.146
  Angle     :  0.791  14.448  10306  Z= 0.370
  Chirality :  0.042   0.292   1148
  Planarity :  0.005   0.062   1337
  Dihedral  :  4.199  38.864   1035
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.46 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.27), residues: 930
  helix:  1.91 (0.21), residues: 620
  sheet:  0.10 (0.91), residues: 35
  loop :  0.43 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1154 
 HIS   0.005   0.001   HIS A 624 
 PHE   0.046   0.002   PHE A 465 
 TYR   0.012   0.001   TYR A 282 
 ARG   0.016   0.001   ARG A1007 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04192 (  484)
  hydrogen bonds       : angle       4.39259 ( 1434)
  covalent geometry    : bond        0.00341 ( 7585)
  covalent geometry    : angle       0.79052 (10306)

*********************** 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
  121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8214 (m)
REVERT: A  263 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7446 (ptp)
REVERT: A  268 MET cc_start: 0.8327 (mpt) cc_final: 0.7979 (mmm)
REVERT: A  280 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8654 (tp)
REVERT: A  297 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8146 (mm)
REVERT: A  321 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7692 (pp20)
REVERT: A  451 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8899 (mm-30)
REVERT: A  482 MET cc_start: 0.8170 (ttm) cc_final: 0.7895 (ptt)
REVERT: A  495 GLU cc_start: 0.9064 (tp30) cc_final: 0.8567 (tm-30)
REVERT: A  621 LEU cc_start: 0.9044 (mt) cc_final: 0.8827 (mt)
REVERT: A  772 MET cc_start: 0.7838 (tmm) cc_final: 0.7382 (tmm)
REVERT: A  805 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7751 (mtp85)
REVERT: A  868 MET cc_start: 0.7619 (tmm) cc_final: 0.6803 (tpp)
REVERT: A  975 MET cc_start: 0.7977 (mmm) cc_final: 0.6955 (ttt)
REVERT: A  992 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7503 (tm-30)
REVERT: A 1042 GLU cc_start: 0.8519 (tp30) cc_final: 0.8250 (tm-30)
REVERT: A 1062 SER cc_start: 0.9154 (m) cc_final: 0.8715 (p)
REVERT: A 1219 LEU cc_start: 0.8177 (tp) cc_final: 0.7856 (mt)
  outliers start: 22
  outliers final: 13
  residues processed: 113
  average time/residue: 1.1961
  time to fit residues: 145.1036
Evaluate side-chains
  109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 64 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0370
   chunk 55 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    1.0260

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.139757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.104721 restraints weight = 42186.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 5.81
r_work: 0.3584 rms_B_bonded: 5.72 restraints_weight: 2.0000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.5897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7585  Z= 0.156
  Angle     :  0.801  13.884  10306  Z= 0.377
  Chirality :  0.042   0.348   1148
  Planarity :  0.005   0.057   1337
  Dihedral  :  4.219  37.853   1035
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.71 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 930
  helix:  1.85 (0.21), residues: 620
  sheet:  0.15 (0.95), residues: 33
  loop :  0.43 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1154 
 HIS   0.007   0.001   HIS A 512 
 PHE   0.026   0.002   PHE A 497 
 TYR   0.022   0.001   TYR A 468 
 ARG   0.011   0.001   ARG A 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  484)
  hydrogen bonds       : angle       4.43270 ( 1434)
  covalent geometry    : bond        0.00368 ( 7585)
  covalent geometry    : angle       0.80122 (10306)

********************** 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
  119 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7507 (ptm)
REVERT: A  268 MET cc_start: 0.8334 (mpt) cc_final: 0.7956 (mmm)
REVERT: A  280 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8494 (mt)
REVERT: A  297 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8157 (mm)
REVERT: A  321 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7669 (pp20)
REVERT: A  372 LYS cc_start: 0.7810 (pmtt) cc_final: 0.7534 (tptp)
REVERT: A  441 TRP cc_start: 0.7923 (m-10) cc_final: 0.7373 (m-90)
REVERT: A  451 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8911 (mm-30)
REVERT: A  482 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7926 (ptt)
REVERT: A  495 GLU cc_start: 0.9086 (tp30) cc_final: 0.8582 (tm-30)
REVERT: A  621 LEU cc_start: 0.9013 (mt) cc_final: 0.8809 (mt)
REVERT: A  683 LEU cc_start: 0.8778 (pt) cc_final: 0.8537 (pt)
REVERT: A  805 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7734 (mtp85)
REVERT: A  868 MET cc_start: 0.7666 (tmm) cc_final: 0.6773 (tpp)
REVERT: A  975 MET cc_start: 0.7990 (mmm) cc_final: 0.6975 (ttt)
REVERT: A  992 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7508 (tm-30)
REVERT: A 1042 GLU cc_start: 0.8520 (tp30) cc_final: 0.8262 (tm-30)
REVERT: A 1219 LEU cc_start: 0.8246 (tp) cc_final: 0.7917 (mt)
  outliers start: 21
  outliers final: 12
  residues processed: 111
  average time/residue: 1.0636
  time to fit residues: 126.9579
Evaluate side-chains
  112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  263 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  915 SER
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue 1019 ASP
Chi-restraints excluded: chain A residue 1029 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0370
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.141686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.106905 restraints weight = 41691.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 5.80
r_work: 0.3618 rms_B_bonded: 5.77 restraints_weight: 2.0000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.6024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7585  Z= 0.144
  Angle     :  0.810  13.871  10306  Z= 0.379
  Chirality :  0.041   0.326   1148
  Planarity :  0.005   0.053   1337
  Dihedral  :  4.239  40.648   1035
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.71 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.27), residues: 930
  helix:  1.85 (0.21), residues: 621
  sheet:  0.25 (0.98), residues: 33
  loop :  0.48 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1154 
 HIS   0.005   0.001   HIS A 624 
 PHE   0.043   0.002   PHE A 465 
 TYR   0.017   0.001   TYR A 468 
 ARG   0.010   0.001   ARG A 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  484)
  hydrogen bonds       : angle       4.40451 ( 1434)
  covalent geometry    : bond        0.00334 ( 7585)
  covalent geometry    : angle       0.80983 (10306)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7147.33 seconds
wall clock time: 130 minutes 10.34 seconds (7810.34 seconds total)