Starting phenix.real_space_refine
on Tue Feb 11 22:05:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d1b_27121/02_2025/8d1b_27121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d1b_27121/02_2025/8d1b_27121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d1b_27121/02_2025/8d1b_27121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d1b_27121/02_2025/8d1b_27121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d1b_27121/02_2025/8d1b_27121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d1b_27121/02_2025/8d1b_27121.cif"
  }
  resolution = 3.57
  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=  -0.001 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4196      2.51       5
     N    1204      2.21       5
     O    1286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6724
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 1379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1379
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 5, 'TRANS': 172}
    Chain: "A"
      Number of atoms: 1983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 1983
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 17, 'TRANS': 241}
          Chain breaks: 1
  Restraints were copied for chains:
    D, B
  Time building chain proxies: 6.31, per 1000 atoms: 0.94
  Number of scatterers: 6724
  At special positions: 0
  Unit cell: (86.355, 88.065, 112.005, 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      38     16.00
     O    1286      8.00
     N    1204      7.00
     C    4196      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 987 " - pdb=" SG  CYS D1014 " distance=2.03

  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 6 sheets defined
      10.3% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'D' and resid 852 through 857
      removed outlier: 4.190A  pdb=" N   VAL D 857 " --> pdb=" O   ILE D 853 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 992 through 996
      removed outlier: 3.983A  pdb=" N   THR D 995 " --> pdb=" O   THR D 992 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 852 through 857
      removed outlier: 4.190A  pdb=" N   VAL C 857 " --> pdb=" O   ILE C 853 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 992 through 996
      removed outlier: 3.983A  pdb=" N   THR C 995 " --> pdb=" O   THR C 992 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 64
      removed outlier: 3.788A  pdb=" N   ALA B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 96
      removed outlier: 3.660A  pdb=" N   GLN B  96 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 105
      removed outlier: 3.720A  pdb=" N   ALA B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA B 105 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 121
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'A' and resid 56 through 64
      removed outlier: 3.787A  pdb=" N   ALA A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 96
      removed outlier: 3.659A  pdb=" N   GLN A  96 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 105
      removed outlier: 3.720A  pdb=" N   ALA A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 136 through 140
    Processing sheet with id=AA1, first strand: chain 'D' and resid 894 through 897
      removed outlier: 3.562A  pdb=" N   GLY D 895 " --> pdb=" O   VAL D 902 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 894 through 897
      removed outlier: 3.562A  pdb=" N   GLY C 895 " --> pdb=" O   VAL C 902 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 249
      removed outlier: 3.590A  pdb=" N   ASP B 271 " --> pdb=" O   ARG B 146 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ARG B 146 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU B 149 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   THR B 173 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 221
      removed outlier: 3.671A  pdb=" N   GLY B 219 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A 173 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 149 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ARG A 146 " --> pdb=" O   ASP A 271 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP A 271 " --> pdb=" O   ARG A 146 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 237
      removed outlier: 3.718A  pdb=" N   GLN B 237 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237
      removed outlier: 3.717A  pdb=" N   GLN A 237 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)

    76 hydrogen bonds defined for protein.
    162 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: 1.43

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2301
        1.34 -     1.46: 1523
        1.46 -     1.58: 2976
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6858
  Sorted by residual:
  bond pdb=" C   GLN A 114 "
       pdb=" N   ALA A 115 "
    ideal  model  delta    sigma   weight residual
    1.331  1.306  0.025 1.73e-02 3.34e+03 2.10e+00
  bond pdb=" C   GLN B 114 "
       pdb=" N   ALA B 115 "
    ideal  model  delta    sigma   weight residual
    1.331  1.306  0.025 1.73e-02 3.34e+03 2.02e+00
  bond pdb=" C   ALA B 106 "
       pdb=" N   ASN B 107 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.019 1.38e-02 5.25e+03 1.97e+00
  bond pdb=" C   ALA A 106 "
       pdb=" N   ASN A 107 "
    ideal  model  delta    sigma   weight residual
    1.331  1.313  0.018 1.38e-02 5.25e+03 1.68e+00
  bond pdb=" CB  VAL A 134 "
       pdb=" CG1 VAL A 134 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.63e+00
  ... (remaining 6853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 8475
        1.85 -     3.69: 703
        3.69 -     5.54: 96
        5.54 -     7.39: 16
        7.39 -     9.24: 4
  Bond angle restraints: 9294
  Sorted by residual:
  angle pdb=" N   GLY B  86 "
        pdb=" CA  GLY B  86 "
        pdb=" C   GLY B  86 "
      ideal   model   delta    sigma   weight residual
     113.99  108.54    5.45 1.28e+00 6.10e-01 1.81e+01
  angle pdb=" N   GLY A  86 "
        pdb=" CA  GLY A  86 "
        pdb=" C   GLY A  86 "
      ideal   model   delta    sigma   weight residual
     113.99  108.55    5.44 1.28e+00 6.10e-01 1.81e+01
  angle pdb=" N   LYS B 257 "
        pdb=" CA  LYS B 257 "
        pdb=" C   LYS B 257 "
      ideal   model   delta    sigma   weight residual
     109.83  104.83    5.00 1.27e+00 6.20e-01 1.55e+01
  angle pdb=" N   LYS A 257 "
        pdb=" CA  LYS A 257 "
        pdb=" C   LYS A 257 "
      ideal   model   delta    sigma   weight residual
     109.83  104.88    4.95 1.27e+00 6.20e-01 1.52e+01
  angle pdb=" CA  LEU B  71 "
        pdb=" C   LEU B  71 "
        pdb=" N   SER B  72 "
      ideal   model   delta    sigma   weight residual
     114.17  119.36   -5.19 1.45e+00 4.76e-01 1.28e+01
  ... (remaining 9289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 3660
       17.78 -    35.56: 381
       35.56 -    53.34: 56
       53.34 -    71.13: 6
       71.13 -    88.91: 4
  Dihedral angle restraints: 4107
    sinusoidal: 1635
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CA  ARG C 886 "
           pdb=" C   ARG C 886 "
           pdb=" N   PRO C 887 "
           pdb=" CA  PRO C 887 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.22  -27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  ARG D 886 "
           pdb=" C   ARG D 886 "
           pdb=" N   PRO D 887 "
           pdb=" CA  PRO D 887 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.27  -27.73     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  GLU A 263 "
           pdb=" C   GLU A 263 "
           pdb=" N   VAL A 264 "
           pdb=" CA  VAL A 264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.46  -25.54     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 4104 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 550
       0.037 -    0.073: 308
       0.073 -    0.109: 119
       0.109 -    0.146: 23
       0.146 -    0.182: 10
  Chirality restraints: 1010
  Sorted by residual:
  chirality pdb=" CA  PRO D 887 "
            pdb=" N   PRO D 887 "
            pdb=" C   PRO D 887 "
            pdb=" CB  PRO D 887 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.32e-01
  chirality pdb=" CA  PRO C 887 "
            pdb=" N   PRO C 887 "
            pdb=" C   PRO C 887 "
            pdb=" CB  PRO C 887 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.20e-01
  chirality pdb=" CB  THR B 173 "
            pdb=" CA  THR B 173 "
            pdb=" OG1 THR B 173 "
            pdb=" CG2 THR B 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 1007 not shown)

  Planarity restraints: 1232
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  92 "   -0.055 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO A  93 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  92 "    0.055 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO B  93 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO B  93 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B  93 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 257 "   -0.046 5.00e-02 4.00e+02   6.96e-02 7.75e+00
        pdb=" N   PRO B 258 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 258 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 258 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1229 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 106
        2.60 -     3.18: 6070
        3.18 -     3.75: 9159
        3.75 -     4.33: 13116
        4.33 -     4.90: 21669
  Nonbonded interactions: 50120
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A  76 "
            pdb=" SG  CYS A 236 "
     model   vdw
     2.025 3.760
  nonbonded pdb=" SG  CYS B  76 "
            pdb=" SG  CYS B 236 "
     model   vdw
     2.025 3.760
  nonbonded pdb=" SG  CYS A 295 "
            pdb=" SG  CYS A 317 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 295 "
            pdb=" SG  CYS B 317 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS A 282 "
            pdb=" SG  CYS A 302 "
     model   vdw
     2.031 3.760
  ... (remaining 50115 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.050
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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      :  0.006   0.042   6858  Z= 0.405
  Angle     :  1.086   9.237   9294  Z= 0.620
  Chirality :  0.052   0.182   1010
  Planarity :  0.008   0.084   1232
  Dihedral  : 14.425  88.908   2532
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 24.13 %
    Favored  : 75.87 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.28 %
    Favored  : 99.45 %
  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: -6.32 (0.22), residues: 862
  helix: -5.21 (0.17), residues: 100
  sheet: -3.30 (0.35), residues: 164
  loop : -4.63 (0.20), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 182 
 HIS   0.003   0.001   HIS D 926 
 PHE   0.013   0.002   PHE D 868 
 TYR   0.023   0.002   TYR A  62 
 ARG   0.005   0.001   ARG A 265 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.764 
Fit side-chains
REVERT: D  965 TYR cc_start: 0.8098 (m-80) cc_final: 0.7772 (m-80)
REVERT: D  998 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6789 (m90)
REVERT: D 1010 ASN cc_start: 0.8319 (t0) cc_final: 0.8105 (t0)
REVERT: C  965 TYR cc_start: 0.8096 (m-80) cc_final: 0.7685 (m-80)
REVERT: C  998 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6721 (m90)
  outliers start: 2
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1413
  time to fit residues: 26.0487
Evaluate side-chains
  102 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  998 HIS
Chi-restraints excluded: chain C residue  998 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0070
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
D 990 HIS
C 990 HIS
B 161 GLN
B 165 GLN
B 237 GLN
A 161 GLN
A 165 GLN
A 237 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.152303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.122166 restraints weight = 10386.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.125906 restraints weight = 6214.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.128363 restraints weight = 4498.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6858  Z= 0.239
  Angle     :  0.833   8.534   9294  Z= 0.420
  Chirality :  0.048   0.204   1010
  Planarity :  0.007   0.072   1232
  Dihedral  :  7.068  26.302    962
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.77 %
    Favored  : 79.23 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.83 %
    Favored  : 89.06 %
  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: -5.82 (0.23), residues: 862
  helix: -4.73 (0.27), residues: 90
  sheet: -2.83 (0.37), residues: 168
  loop : -4.39 (0.21), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 288 
 HIS   0.006   0.001   HIS D 990 
 PHE   0.008   0.001   PHE C 865 
 TYR   0.021   0.002   TYR A  62 
 ARG   0.005   0.001   ARG D 861 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.607 
Fit side-chains
REVERT: D  905 TYR cc_start: 0.8813 (p90) cc_final: 0.8545 (p90)
REVERT: D  955 MET cc_start: 0.6346 (ptt) cc_final: 0.6067 (ptt)
REVERT: D  965 TYR cc_start: 0.7809 (m-80) cc_final: 0.7517 (m-80)
REVERT: D 1010 ASN cc_start: 0.8466 (t0) cc_final: 0.8023 (t0)
REVERT: C  965 TYR cc_start: 0.7852 (m-80) cc_final: 0.7627 (m-80)
REVERT: C  975 HIS cc_start: 0.6910 (m-70) cc_final: 0.6709 (m170)
REVERT: C 1010 ASN cc_start: 0.8740 (t0) cc_final: 0.8345 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 127
  average time/residue: 0.1480
  time to fit residues: 26.8637
Evaluate side-chains
  105 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  941 VAL
Chi-restraints excluded: chain C residue  990 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0040
   chunk 52 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
D 990 HIS
C 990 HIS
B 237 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.155132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.126074 restraints weight = 10792.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.129356 restraints weight = 6846.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131481 restraints weight = 5170.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6858  Z= 0.247
  Angle     :  0.799   8.055   9294  Z= 0.401
  Chirality :  0.046   0.209   1010
  Planarity :  0.006   0.069   1232
  Dihedral  :  6.612  26.964    958
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.98 %
    Favored  : 82.02 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.24 %
    Favored  : 83.24 %
  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: -5.64 (0.23), residues: 862
  helix: -4.39 (0.31), residues: 90
  sheet: -2.78 (0.36), residues: 168
  loop : -4.27 (0.21), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 288 
 HIS   0.004   0.001   HIS C 990 
 PHE   0.007   0.001   PHE D 868 
 TYR   0.015   0.002   TYR B  80 
 ARG   0.006   0.000   ARG C 880 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.770 
Fit side-chains
REVERT: D  905 TYR cc_start: 0.8868 (p90) cc_final: 0.8565 (p90)
REVERT: D  911 VAL cc_start: 0.9209 (t) cc_final: 0.8960 (p)
REVERT: D 1010 ASN cc_start: 0.8238 (t0) cc_final: 0.7750 (t0)
REVERT: C 1010 ASN cc_start: 0.8513 (t0) cc_final: 0.7941 (t0)
REVERT: A   81 GLU cc_start: 0.8179 (mp0) cc_final: 0.7962 (mp0)
REVERT: A  205 ASP cc_start: 0.8013 (t0) cc_final: 0.7756 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1476
  time to fit residues: 24.9826
Evaluate side-chains
  110 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  990 HIS
Chi-restraints excluded: chain B residue   76 CYS
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain A residue   76 CYS
Chi-restraints excluded: chain A residue  101 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    0.0030
   chunk 63 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0070
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0970
   chunk 70 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0040
   overall best weight:    0.1018

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

Flipped N/Q/H residues before XYZ refinement:
D 990 HIS
C 975 HIS
C 990 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.159938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.131101 restraints weight = 10642.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.134520 restraints weight = 6669.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.136742 restraints weight = 4981.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6858  Z= 0.205
  Angle     :  0.762   8.599   9294  Z= 0.376
  Chirality :  0.045   0.210   1010
  Planarity :  0.005   0.065   1232
  Dihedral  :  6.134  27.822    958
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.94 %
    Favored  : 83.06 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.28 %
    Favored  : 79.09 %
  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: -5.53 (0.24), residues: 862
  helix: -4.33 (0.29), residues: 98
  sheet: -2.97 (0.33), residues: 202
  loop : -4.07 (0.22), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 288 
 HIS   0.001   0.000   HIS D 975 
 PHE   0.007   0.001   PHE C 991 
 TYR   0.013   0.001   TYR B  80 
 ARG   0.003   0.000   ARG B 240 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.697 
Fit side-chains
REVERT: D  905 TYR cc_start: 0.8850 (p90) cc_final: 0.8648 (p90)
REVERT: D  911 VAL cc_start: 0.9101 (t) cc_final: 0.8832 (p)
REVERT: D  975 HIS cc_start: 0.6474 (m-70) cc_final: 0.6269 (m170)
REVERT: D 1010 ASN cc_start: 0.8176 (t0) cc_final: 0.7668 (t0)
REVERT: C  902 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8297 (m)
REVERT: C 1010 ASN cc_start: 0.8471 (t0) cc_final: 0.7883 (t0)
REVERT: B   88 MET cc_start: 0.6148 (mmp) cc_final: 0.5841 (mmm)
REVERT: A   88 MET cc_start: 0.6030 (mmp) cc_final: 0.5725 (mmm)
REVERT: A  205 ASP cc_start: 0.7877 (t0) cc_final: 0.7673 (t0)
  outliers start: 19
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1411
  time to fit residues: 26.5839
Evaluate side-chains
  115 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  941 VAL
Chi-restraints excluded: chain D residue  989 SER
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  902 VAL
Chi-restraints excluded: chain C residue  941 VAL
Chi-restraints excluded: chain C residue  989 SER
Chi-restraints excluded: chain C residue  990 HIS
Chi-restraints excluded: chain B residue   76 CYS
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0170
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.7822

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

Flipped N/Q/H residues before XYZ refinement:
D 990 HIS
C 990 HIS
B 237 GLN
A 237 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.155732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.126745 restraints weight = 10643.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.130038 restraints weight = 6788.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.132185 restraints weight = 5115.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6858  Z= 0.275
  Angle     :  0.785   9.176   9294  Z= 0.384
  Chirality :  0.046   0.216   1010
  Planarity :  0.006   0.064   1232
  Dihedral  :  6.016  26.834    958
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.87 %
    Favored  : 82.13 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.01 %
    Favored  : 79.09 %
  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: -5.38 (0.24), residues: 862
  helix: -4.22 (0.32), residues: 96
  sheet: -2.83 (0.34), residues: 198
  loop : -4.00 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 245 
 HIS   0.010   0.001   HIS D 990 
 PHE   0.007   0.001   PHE A 253 
 TYR   0.008   0.001   TYR D 905 
 ARG   0.003   0.000   ARG B 265 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: D  880 ARG cc_start: 0.8356 (ttt90) cc_final: 0.7896 (tmt-80)
REVERT: D  905 TYR cc_start: 0.8852 (p90) cc_final: 0.8596 (p90)
REVERT: D 1010 ASN cc_start: 0.8213 (t0) cc_final: 0.7308 (t0)
REVERT: C 1010 ASN cc_start: 0.8423 (t0) cc_final: 0.7769 (t0)
  outliers start: 21
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1465
  time to fit residues: 25.5561
Evaluate side-chains
  109 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  989 SER
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  990 HIS
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain A residue   76 CYS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0570
   chunk 32 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
D 990 HIS
C 990 HIS
B 237 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.157167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.128611 restraints weight = 10608.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.131928 restraints weight = 6741.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.134061 restraints weight = 5064.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6858  Z= 0.225
  Angle     :  0.756   9.917   9294  Z= 0.371
  Chirality :  0.045   0.205   1010
  Planarity :  0.005   0.063   1232
  Dihedral  :  5.840  26.292    958
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.52 %
    Favored  : 82.48 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.22 %
    Favored  : 77.70 %
  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: -5.23 (0.25), residues: 862
  helix: -4.07 (0.34), residues: 96
  sheet: -2.65 (0.35), residues: 198
  loop : -3.94 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 245 
 HIS   0.005   0.001   HIS C 990 
 PHE   0.007   0.001   PHE B 253 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.003   0.000   ARG A 265 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: D  880 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7860 (tmt-80)
REVERT: D 1010 ASN cc_start: 0.8316 (t0) cc_final: 0.7892 (t0)
REVERT: C 1010 ASN cc_start: 0.8433 (t0) cc_final: 0.7721 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 120
  average time/residue: 0.1551
  time to fit residues: 26.1682
Evaluate side-chains
  115 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  950 LYS
Chi-restraints excluded: chain C residue  989 SER
Chi-restraints excluded: chain B residue   76 CYS
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0040
   chunk 22 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
D 975 HIS
D 990 HIS
B 237 GLN
A 237 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.157693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.128907 restraints weight = 10601.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131981 restraints weight = 6741.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.134219 restraints weight = 5144.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6858  Z= 0.234
  Angle     :  0.750  10.376   9294  Z= 0.370
  Chirality :  0.044   0.208   1010
  Planarity :  0.005   0.062   1232
  Dihedral  :  5.767  25.439    958
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.52 %
    Favored  : 82.48 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.08 %
    Favored  : 77.15 %
  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: -5.11 (0.25), residues: 862
  helix: -3.91 (0.36), residues: 96
  sheet: -2.53 (0.35), residues: 198
  loop : -3.89 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 288 
 HIS   0.005   0.001   HIS D 990 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.008   0.001   TYR C 980 
 ARG   0.002   0.000   ARG A 265 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.811 
Fit side-chains
REVERT: D  880 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7886 (tmt-80)
REVERT: D 1010 ASN cc_start: 0.8313 (t0) cc_final: 0.7867 (t0)
REVERT: C 1010 ASN cc_start: 0.8462 (t0) cc_final: 0.7925 (t0)
  outliers start: 20
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1568
  time to fit residues: 26.2539
Evaluate side-chains
  109 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain D residue  989 SER
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  892 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 76 optimal weight:    0.2980
   chunk 46 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
D 990 HIS
A 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.154956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124343 restraints weight = 10455.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.128163 restraints weight = 6140.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.130706 restraints weight = 4437.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6858  Z= 0.246
  Angle     :  0.770  10.658   9294  Z= 0.380
  Chirality :  0.044   0.205   1010
  Planarity :  0.005   0.062   1232
  Dihedral  :  5.741  25.614    958
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.75 %
    Favored  : 82.25 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.94 %
    Favored  : 77.01 %
  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: -4.97 (0.25), residues: 862
  helix: -3.83 (0.37), residues: 96
  sheet: -2.00 (0.39), residues: 164
  loop : -3.90 (0.22), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 245 
 HIS   0.004   0.001   HIS D 990 
 PHE   0.007   0.001   PHE D 840 
 TYR   0.014   0.001   TYR B  80 
 ARG   0.004   0.000   ARG C 978 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: D  880 ARG cc_start: 0.8306 (ttt90) cc_final: 0.7871 (tmt-80)
REVERT: D 1010 ASN cc_start: 0.8409 (t0) cc_final: 0.7806 (t0)
REVERT: C  905 TYR cc_start: 0.8867 (p90) cc_final: 0.8551 (p90)
REVERT: C 1010 ASN cc_start: 0.8543 (t0) cc_final: 0.7813 (t0)
  outliers start: 22
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1589
  time to fit residues: 26.1252
Evaluate side-chains
  114 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  892 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  253 PHE
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0070
   chunk 54 optimal weight:    0.1980
   chunk 52 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4800

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
A 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.156894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.126137 restraints weight = 10486.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.130139 restraints weight = 6066.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.132738 restraints weight = 4340.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6858  Z= 0.224
  Angle     :  0.747  10.587   9294  Z= 0.369
  Chirality :  0.044   0.203   1010
  Planarity :  0.005   0.061   1232
  Dihedral  :  5.703  25.202    958
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.17 %
    Favored  : 82.83 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.64 %
    Favored  : 76.59 %
  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: -4.94 (0.25), residues: 862
  helix: -3.69 (0.39), residues: 96
  sheet: -2.39 (0.34), residues: 202
  loop : -3.80 (0.23), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 879 
 HIS   0.001   0.001   HIS C 990 
 PHE   0.008   0.001   PHE D 840 
 TYR   0.009   0.001   TYR B  80 
 ARG   0.003   0.000   ARG B 265 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.737 
Fit side-chains
REVERT: D  880 ARG cc_start: 0.8266 (ttt90) cc_final: 0.7870 (tmt-80)
REVERT: D 1010 ASN cc_start: 0.8397 (t0) cc_final: 0.7780 (t0)
REVERT: C  905 TYR cc_start: 0.8827 (p90) cc_final: 0.8573 (p90)
REVERT: C 1010 ASN cc_start: 0.8517 (t0) cc_final: 0.7847 (t0)
REVERT: B  297 LEU cc_start: 0.4643 (OUTLIER) cc_final: 0.4406 (pp)
REVERT: A  297 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4383 (pp)
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1690
  time to fit residues: 27.4532
Evaluate side-chains
  111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  878 LEU
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  892 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  253 PHE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  237 GLN
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0270
   chunk 15 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 78 optimal weight:    0.2980
   chunk 68 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.157210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.125651 restraints weight = 10479.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.129674 restraints weight = 6108.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.132338 restraints weight = 4400.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6858  Z= 0.228
  Angle     :  0.784  12.383   9294  Z= 0.381
  Chirality :  0.044   0.203   1010
  Planarity :  0.005   0.062   1232
  Dihedral  :  5.639  25.191    958
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.71 %
    Favored  : 83.29 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.19 %
    Favored  : 76.32 %
  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: -4.87 (0.25), residues: 862
  helix: -3.64 (0.40), residues: 96
  sheet: -2.33 (0.34), residues: 202
  loop : -3.75 (0.23), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 879 
 HIS   0.001   0.001   HIS C 975 
 PHE   0.009   0.001   PHE D 840 
 TYR   0.008   0.001   TYR B  80 
 ARG   0.004   0.000   ARG A 242 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.677 
Fit side-chains
REVERT: D  880 ARG cc_start: 0.8220 (ttt90) cc_final: 0.7865 (tmt-80)
REVERT: D  954 MET cc_start: 0.6187 (tmm) cc_final: 0.5913 (tmm)
REVERT: D 1010 ASN cc_start: 0.8415 (t0) cc_final: 0.7825 (t0)
REVERT: C  905 TYR cc_start: 0.8814 (p90) cc_final: 0.8547 (p90)
REVERT: C  954 MET cc_start: 0.5989 (tmm) cc_final: 0.5679 (tmm)
REVERT: C 1010 ASN cc_start: 0.8540 (t0) cc_final: 0.7856 (t0)
REVERT: B  297 LEU cc_start: 0.4635 (OUTLIER) cc_final: 0.4408 (pp)
REVERT: A  297 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.4394 (pp)
  outliers start: 18
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1521
  time to fit residues: 24.0297
Evaluate side-chains
  114 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  878 LEU
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  892 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  253 PHE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0870
   chunk 48 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0470
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
D 863 ASN
A 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.166769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.137327 restraints weight = 9622.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.140927 restraints weight = 6095.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143095 restraints weight = 4604.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6858  Z= 0.233
  Angle     :  0.778  11.943   9294  Z= 0.377
  Chirality :  0.044   0.202   1010
  Planarity :  0.005   0.062   1232
  Dihedral  :  5.583  24.643    958
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.87 %
    Favored  : 82.13 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 21.33 %
    Favored  : 76.04 %
  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: -4.72 (0.25), residues: 862
  helix: -3.65 (0.39), residues: 96
  sheet: -2.07 (0.35), residues: 192
  loop : -3.68 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 879 
 HIS   0.001   0.001   HIS D 975 
 PHE   0.008   0.001   PHE D 840 
 TYR   0.010   0.001   TYR D 980 
 ARG   0.003   0.000   ARG B 265 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2467.61 seconds
wall clock time: 45 minutes 2.79 seconds (2702.79 seconds total)