Starting phenix.real_space_refine
on Tue Mar  3 15:42:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d1b_27121/03_2026/8d1b_27121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d1b_27121/03_2026/8d1b_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_27121/03_2026/8d1b_27121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2026/8d1b_27121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2026/8d1b_27121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2026/8d1b_27121.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.041
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6724
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      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: "B"
      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:
    C, A
  Time building chain proxies: 1.73, per 1000 atoms: 0.26
  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=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 987 " - pdb=" SG  CYS D1014 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 987 " - pdb=" SG  CYS C1014 " 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: 0.52
  Conformation dependent library (CDL) restraints added in 354.5 milliseconds
  

  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: 0.18
  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: 0.80

  Time building geometry restraints manager: 0.71 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: 382
       35.56 -    53.34: 58
       53.34 -    71.13: 6
       71.13 -    88.91: 4
  Dihedral angle restraints: 4110
    sinusoidal: 1638
      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 4107 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: 105
        2.60 -     3.18: 6068
        3.18 -     3.75: 9159
        3.75 -     4.33: 13116
        4.33 -     4.90: 21669
  Nonbonded interactions: 50117
  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 50112 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             7.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.520
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.050
-------------------------------------------------------------------------------
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   6860  Z= 0.284
  Angle     :  1.087   9.237   9298  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 : 19.79
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG A 265 
 TYR   0.023   0.002   TYR A  62 
 PHE   0.013   0.002   PHE D 868 
 TRP   0.009   0.002   TRP A 182 
 HIS   0.003   0.001   HIS D 926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 6858)
  covalent geometry    : angle       1.08614 ( 9294)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       2.22214 (    4)
  hydrogen bonds       : bond        0.33497 (   76)
  hydrogen bonds       : angle      13.08484 (  162)

*********************** 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  : 0.261 
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: 0.0598
  time to fit residues: 11.2674
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  : 0.265 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 165 GLN
A 237 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.159636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.130211 restraints weight = 10057.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.133515 restraints weight = 6660.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.135672 restraints weight = 5136.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.137048 restraints weight = 4339.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.138015 restraints weight = 3881.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6860  Z= 0.195
  Angle     :  0.868   8.686   9298  Z= 0.438
  Chirality :  0.049   0.210   1010
  Planarity :  0.007   0.075   1232
  Dihedral  :  7.225  26.220    962
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.23 %
    Favored  : 78.77 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.66 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.86 (0.23), residues: 862
  helix: -4.87 (0.23), residues: 90
  sheet: -2.86 (0.37), residues: 164
  loop : -4.38 (0.21), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 861 
 TYR   0.021   0.002   TYR A  62 
 PHE   0.011   0.002   PHE D 868 
 TRP   0.008   0.001   TRP B 245 
 HIS   0.005   0.001   HIS C 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6858)
  covalent geometry    : angle       0.86742 ( 9294)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       1.86782 (    4)
  hydrogen bonds       : bond        0.03921 (   76)
  hydrogen bonds       : angle       7.74563 (  162)

*********************** 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
  120 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.203 
Fit side-chains
REVERT: D  905 TYR cc_start: 0.8905 (p90) cc_final: 0.8587 (p90)
REVERT: D  965 TYR cc_start: 0.7944 (m-80) cc_final: 0.7666 (m-80)
REVERT: D 1010 ASN cc_start: 0.8234 (t0) cc_final: 0.7925 (t0)
REVERT: C  965 TYR cc_start: 0.8008 (m-80) cc_final: 0.7690 (m-80)
REVERT: C 1010 ASN cc_start: 0.8450 (t0) cc_final: 0.8155 (t0)
REVERT: B   81 GLU cc_start: 0.8023 (mp0) cc_final: 0.7822 (mp0)
  outliers start: 8
  outliers final: 2
  residues processed: 116
  average time/residue: 0.0638
  time to fit residues: 10.7183
Evaluate side-chains
  101 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  990 HIS
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 5 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0270
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0010
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 78 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.4646

-------------------------------------------------------------------------------
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
B 237 GLN
A 161 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.154918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.126489 restraints weight = 10613.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.129729 restraints weight = 6794.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131829 restraints weight = 5132.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.133084 restraints weight = 4286.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.134153 restraints weight = 3815.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6860  Z= 0.154
  Angle     :  0.798   8.510   9298  Z= 0.402
  Chirality :  0.046   0.208   1010
  Planarity :  0.006   0.070   1232
  Dihedral  :  6.654  27.428    958
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.33 %
    Favored  : 81.67 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.37 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.70 (0.23), residues: 862
  helix: -4.61 (0.27), residues: 90
  sheet: -2.78 (0.36), residues: 168
  loop : -4.29 (0.21), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 240 
 TYR   0.014   0.001   TYR B  62 
 PHE   0.007   0.001   PHE D 868 
 TRP   0.006   0.001   TRP A 288 
 HIS   0.006   0.001   HIS D 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6858)
  covalent geometry    : angle       0.79658 ( 9294)
  SS BOND              : bond        0.00668 (    2)
  SS BOND              : angle       2.17891 (    4)
  hydrogen bonds       : bond        0.03134 (   76)
  hydrogen bonds       : angle       6.40318 (  162)

*********************** 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
  125 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.236 
Fit side-chains
REVERT: D  905 TYR cc_start: 0.8865 (p90) cc_final: 0.8616 (p90)
REVERT: D  911 VAL cc_start: 0.9192 (t) cc_final: 0.8963 (p)
REVERT: D 1010 ASN cc_start: 0.8208 (t0) cc_final: 0.7740 (t0)
REVERT: C 1010 ASN cc_start: 0.8441 (t0) cc_final: 0.7865 (t0)
REVERT: A  205 ASP cc_start: 0.7976 (t0) cc_final: 0.7745 (t0)
REVERT: A  263 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6610 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 123
  average time/residue: 0.0640
  time to fit residues: 11.7480
Evaluate side-chains
  111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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 A residue   76 CYS
Chi-restraints excluded: chain A residue  263 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0170
   chunk 17 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8220

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.153268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.124781 restraints weight = 10766.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.128031 restraints weight = 6787.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.130125 restraints weight = 5084.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.131488 restraints weight = 4223.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.132239 restraints weight = 3735.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6860  Z= 0.181
  Angle     :  0.811   7.882   9298  Z= 0.402
  Chirality :  0.046   0.216   1010
  Planarity :  0.006   0.069   1232
  Dihedral  :  6.394  26.919    958
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.61 %
    Favored  : 80.39 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.62 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.61 (0.24), residues: 862
  helix: -4.43 (0.28), residues: 98
  sheet: -2.80 (0.35), residues: 184
  loop : -4.22 (0.22), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 880 
 TYR   0.010   0.001   TYR A  80 
 PHE   0.009   0.001   PHE D 868 
 TRP   0.006   0.001   TRP B 245 
 HIS   0.007   0.001   HIS C 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6858)
  covalent geometry    : angle       0.81081 ( 9294)
  SS BOND              : bond        0.00559 (    2)
  SS BOND              : angle       1.75334 (    4)
  hydrogen bonds       : bond        0.02739 (   76)
  hydrogen bonds       : angle       6.17151 (  162)

*********************** 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
  128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.236 
Fit side-chains
REVERT: D  902 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8437 (m)
REVERT: D  905 TYR cc_start: 0.8900 (p90) cc_final: 0.8626 (p90)
REVERT: D  911 VAL cc_start: 0.9134 (t) cc_final: 0.8868 (p)
REVERT: D 1010 ASN cc_start: 0.8208 (t0) cc_final: 0.7690 (t0)
REVERT: C  902 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8384 (m)
REVERT: C 1010 ASN cc_start: 0.8345 (t0) cc_final: 0.7653 (t0)
REVERT: B   88 MET cc_start: 0.5892 (mmp) cc_final: 0.5609 (mmm)
REVERT: A   88 MET cc_start: 0.5890 (mmp) cc_final: 0.5611 (mmm)
  outliers start: 23
  outliers final: 9
  residues processed: 123
  average time/residue: 0.0633
  time to fit residues: 11.5227
Evaluate side-chains
  116 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  902 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  989 SER
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 B residue  311 VAL
Chi-restraints excluded: chain A 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 47 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0570
   chunk 2 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.9302

-------------------------------------------------------------------------------
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 = 0.3957 r_free = 0.3957 target = 0.150782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120228 restraints weight = 10759.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.124043 restraints weight = 6297.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126535 restraints weight = 4556.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.128162 restraints weight = 3697.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.129181 restraints weight = 3223.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6860  Z= 0.184
  Angle     :  0.811   8.676   9298  Z= 0.398
  Chirality :  0.047   0.214   1010
  Planarity :  0.006   0.068   1232
  Dihedral  :  6.257  26.556    958
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.14 %
    Favored  : 80.86 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 16.34 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.49 (0.24), residues: 862
  helix: -4.30 (0.30), residues: 98
  sheet: -2.68 (0.36), residues: 184
  loop : -4.16 (0.22), residues: 580

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 6858)
  covalent geometry    : angle       0.81041 ( 9294)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       1.29462 (    4)
  hydrogen bonds       : bond        0.02712 (   76)
  hydrogen bonds       : angle       6.07559 (  162)

*********************** 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
  139 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.304 
Fit side-chains
REVERT: D  902 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8320 (m)
REVERT: D  905 TYR cc_start: 0.8870 (p90) cc_final: 0.8604 (p90)
REVERT: D 1010 ASN cc_start: 0.8271 (t0) cc_final: 0.7304 (t0)
REVERT: C  902 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (m)
REVERT: C 1010 ASN cc_start: 0.8445 (t0) cc_final: 0.7777 (t0)
REVERT: B   88 MET cc_start: 0.6130 (mmp) cc_final: 0.5849 (mmm)
REVERT: B  205 ASP cc_start: 0.8139 (t0) cc_final: 0.7887 (t0)
REVERT: A   88 MET cc_start: 0.6162 (mmp) cc_final: 0.5861 (mmm)
REVERT: A  205 ASP cc_start: 0.8174 (t0) cc_final: 0.7914 (t0)
  outliers start: 28
  outliers final: 9
  residues processed: 137
  average time/residue: 0.0601
  time to fit residues: 12.1767
Evaluate side-chains
  117 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain C residue  902 VAL
Chi-restraints excluded: chain B residue   76 CYS
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  237 GLN
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  134 VAL
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 36 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.150964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.121163 restraints weight = 10725.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.124831 restraints weight = 6289.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127206 restraints weight = 4535.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.128716 restraints weight = 3694.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.129653 restraints weight = 3232.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6860  Z= 0.170
  Angle     :  0.798   9.660   9298  Z= 0.392
  Chirality :  0.046   0.215   1010
  Planarity :  0.006   0.066   1232
  Dihedral  :  6.169  26.509    958
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.72 %
    Favored  : 80.28 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.70 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.35 (0.24), residues: 862
  helix: -4.05 (0.33), residues: 98
  sheet: -2.56 (0.36), residues: 184
  loop : -4.10 (0.22), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 861 
 TYR   0.012   0.001   TYR A  80 
 PHE   0.008   0.001   PHE A 253 
 TRP   0.006   0.001   TRP B 245 
 HIS   0.002   0.001   HIS D 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6858)
  covalent geometry    : angle       0.79732 ( 9294)
  SS BOND              : bond        0.00464 (    2)
  SS BOND              : angle       1.45361 (    4)
  hydrogen bonds       : bond        0.02530 (   76)
  hydrogen bonds       : angle       5.92734 (  162)

*********************** 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
  131 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.262 
Fit side-chains
REVERT: D  902 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8308 (m)
REVERT: D  905 TYR cc_start: 0.8869 (p90) cc_final: 0.8596 (p90)
REVERT: D  950 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7366 (tttt)
REVERT: D 1010 ASN cc_start: 0.8424 (t0) cc_final: 0.7977 (t0)
REVERT: C  902 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8239 (m)
REVERT: C  950 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7413 (tttt)
REVERT: C  979 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7174 (pm20)
REVERT: C 1010 ASN cc_start: 0.8429 (t0) cc_final: 0.7613 (t0)
REVERT: B  205 ASP cc_start: 0.8115 (t0) cc_final: 0.7860 (t0)
REVERT: B  297 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.4149 (pp)
REVERT: A  205 ASP cc_start: 0.8119 (t0) cc_final: 0.7875 (t0)
REVERT: A  297 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.4040 (pp)
  outliers start: 27
  outliers final: 13
  residues processed: 126
  average time/residue: 0.0634
  time to fit residues: 11.6143
Evaluate side-chains
  121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  950 LYS
Chi-restraints excluded: chain D residue  990 HIS
Chi-restraints excluded: chain C residue  902 VAL
Chi-restraints excluded: chain C residue  950 LYS
Chi-restraints excluded: chain C residue  979 GLN
Chi-restraints excluded: chain C residue  990 HIS
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   76 CYS
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  134 VAL
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   76 CYS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  297 LEU
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 15 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0050
   chunk 57 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.152441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.122748 restraints weight = 10559.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.126465 restraints weight = 6174.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128887 restraints weight = 4441.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.130458 restraints weight = 3599.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.131461 restraints weight = 3133.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6860  Z= 0.150
  Angle     :  0.771  10.124   9298  Z= 0.380
  Chirality :  0.045   0.206   1010
  Planarity :  0.005   0.065   1232
  Dihedral  :  6.003  26.078    958
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.21 %
    Favored  : 81.79 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.50 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.26 (0.25), residues: 862
  helix: -3.81 (0.38), residues: 96
  sheet: -2.75 (0.34), residues: 202
  loop : -3.98 (0.23), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 861 
 TYR   0.013   0.001   TYR B  80 
 PHE   0.007   0.001   PHE C 840 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.004   0.001   HIS D 975 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6858)
  covalent geometry    : angle       0.77079 ( 9294)
  SS BOND              : bond        0.00267 (    2)
  SS BOND              : angle       1.28193 (    4)
  hydrogen bonds       : bond        0.02321 (   76)
  hydrogen bonds       : angle       5.64131 (  162)

*********************** 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
  127 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.268 
Fit side-chains
REVERT: D  905 TYR cc_start: 0.8861 (p90) cc_final: 0.8569 (p90)
REVERT: D  950 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7363 (tttt)
REVERT: D  975 HIS cc_start: 0.6137 (m-70) cc_final: 0.5918 (m170)
REVERT: D 1010 ASN cc_start: 0.8363 (t0) cc_final: 0.7911 (t0)
REVERT: C  902 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8252 (m)
REVERT: C  950 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7377 (tttt)
REVERT: C  979 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7052 (pm20)
REVERT: C 1010 ASN cc_start: 0.8448 (t0) cc_final: 0.7810 (t0)
REVERT: B   76 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7160 (t)
REVERT: B  205 ASP cc_start: 0.8101 (t0) cc_final: 0.7824 (t0)
REVERT: B  297 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4240 (pp)
REVERT: A   76 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7077 (t)
REVERT: A  205 ASP cc_start: 0.8097 (t0) cc_final: 0.7860 (t0)
REVERT: A  224 THR cc_start: 0.8560 (t) cc_final: 0.8283 (m)
REVERT: A  297 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.4131 (pp)
  outliers start: 22
  outliers final: 6
  residues processed: 123
  average time/residue: 0.0649
  time to fit residues: 11.6721
Evaluate side-chains
  121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ILE
Chi-restraints excluded: chain D residue  950 LYS
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  902 VAL
Chi-restraints excluded: chain C residue  950 LYS
Chi-restraints excluded: chain C residue  979 GLN
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   76 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   76 CYS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  297 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 14 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0010
   chunk 63 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0070
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0050
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.2818

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.156956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126588 restraints weight = 10600.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.130592 restraints weight = 6125.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.133195 restraints weight = 4373.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.134869 restraints weight = 3520.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.135752 restraints weight = 3055.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6860  Z= 0.124
  Angle     :  0.738  11.061   9298  Z= 0.361
  Chirality :  0.044   0.203   1010
  Planarity :  0.005   0.064   1232
  Dihedral  :  5.684  25.732    958
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.75 %
    Favored  : 82.25 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.50 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.92 (0.25), residues: 862
  helix: -3.50 (0.42), residues: 96
  sheet: -2.24 (0.36), residues: 186
  loop : -3.86 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 861 
 TYR   0.009   0.001   TYR A 254 
 PHE   0.009   0.001   PHE D 840 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.002   0.000   HIS D 975 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6858)
  covalent geometry    : angle       0.73737 ( 9294)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       1.12130 (    4)
  hydrogen bonds       : bond        0.01972 (   76)
  hydrogen bonds       : angle       5.11497 (  162)

*********************** 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
  133 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.272 
Fit side-chains
REVERT: D  880 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7736 (tmt-80)
REVERT: D  905 TYR cc_start: 0.8793 (p90) cc_final: 0.8590 (p90)
REVERT: D  950 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7243 (tttt)
REVERT: D 1010 ASN cc_start: 0.8381 (t0) cc_final: 0.7768 (t0)
REVERT: C  880 ARG cc_start: 0.8338 (ttt90) cc_final: 0.7878 (tmt-80)
REVERT: C  902 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (m)
REVERT: C  905 TYR cc_start: 0.8883 (p90) cc_final: 0.8564 (p90)
REVERT: C  979 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.7040 (pm20)
REVERT: C 1010 ASN cc_start: 0.8417 (t0) cc_final: 0.7807 (t0)
REVERT: B   76 CYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7175 (t)
REVERT: B  205 ASP cc_start: 0.7977 (t0) cc_final: 0.7745 (t0)
REVERT: B  297 LEU cc_start: 0.4531 (OUTLIER) cc_final: 0.4272 (pp)
REVERT: A   76 CYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7151 (t)
REVERT: A  224 THR cc_start: 0.8526 (t) cc_final: 0.8234 (m)
REVERT: A  297 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.4110 (pp)
  outliers start: 24
  outliers final: 9
  residues processed: 126
  average time/residue: 0.0678
  time to fit residues: 12.1780
Evaluate side-chains
  118 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  950 LYS
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  892 ILE
Chi-restraints excluded: chain C residue  902 VAL
Chi-restraints excluded: chain C residue  950 LYS
Chi-restraints excluded: chain C residue  979 GLN
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   76 CYS
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   76 CYS
Chi-restraints excluded: chain A residue  237 GLN
Chi-restraints excluded: chain A residue  297 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 78 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
D 863 ASN
D 975 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 = 0.4077 r_free = 0.4077 target = 0.163029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133190 restraints weight = 9874.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.136844 restraints weight = 6195.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.139315 restraints weight = 4633.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.140863 restraints weight = 3821.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.141532 restraints weight = 3371.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6860  Z= 0.169
  Angle     :  0.774  11.573   9298  Z= 0.382
  Chirality :  0.045   0.204   1010
  Planarity :  0.006   0.063   1232
  Dihedral  :  5.763  25.426    958
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.98 %
    Favored  : 82.02 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.78 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.88 (0.25), residues: 862
  helix: -3.50 (0.42), residues: 96
  sheet: -2.04 (0.39), residues: 164
  loop : -3.85 (0.22), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 242 
 TYR   0.009   0.001   TYR D 980 
 PHE   0.012   0.002   PHE A 253 
 TRP   0.006   0.001   TRP D 879 
 HIS   0.002   0.001   HIS D 975 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 6858)
  covalent geometry    : angle       0.77407 ( 9294)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       1.28176 (    4)
  hydrogen bonds       : bond        0.02283 (   76)
  hydrogen bonds       : angle       5.35979 (  162)

*********************** 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
  128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.259 
Fit side-chains
REVERT: D 1010 ASN cc_start: 0.8217 (t0) cc_final: 0.7836 (t0)
REVERT: C  905 TYR cc_start: 0.8882 (p90) cc_final: 0.8611 (p90)
REVERT: C 1010 ASN cc_start: 0.8234 (t0) cc_final: 0.7654 (t0)
REVERT: B  297 LEU cc_start: 0.4754 (OUTLIER) cc_final: 0.4517 (pp)
REVERT: A  297 LEU cc_start: 0.4684 (OUTLIER) cc_final: 0.4440 (pp)
  outliers start: 26
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0764
  time to fit residues: 12.7893
Evaluate side-chains
  118 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
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  950 LYS
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  892 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  148 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  134 VAL
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  312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0870
   chunk 55 optimal weight:    0.1980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.156167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.125325 restraints weight = 10240.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.129216 restraints weight = 6082.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.131735 restraints weight = 4433.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.133259 restraints weight = 3627.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134367 restraints weight = 3211.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6860  Z= 0.141
  Angle     :  0.779  11.488   9298  Z= 0.383
  Chirality :  0.044   0.204   1010
  Planarity :  0.005   0.063   1232
  Dihedral  :  5.690  25.465    958
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.63 %
    Favored  : 82.37 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.86 (0.25), residues: 862
  helix: -3.46 (0.43), residues: 96
  sheet: -2.29 (0.35), residues: 192
  loop : -3.78 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.008   0.001   TYR D 980 
 PHE   0.010   0.001   PHE D 840 
 TRP   0.005   0.001   TRP C 879 
 HIS   0.001   0.001   HIS D 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6858)
  covalent geometry    : angle       0.77822 ( 9294)
  SS BOND              : bond        0.00360 (    2)
  SS BOND              : angle       1.43643 (    4)
  hydrogen bonds       : bond        0.02040 (   76)
  hydrogen bonds       : angle       5.22257 (  162)

********************** 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
  118 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.258 
Fit side-chains
REVERT: D  839 GLN cc_start: 0.6404 (mt0) cc_final: 0.6194 (mt0)
REVERT: D  880 ARG cc_start: 0.8212 (ttt90) cc_final: 0.7721 (tmt-80)
REVERT: D  954 MET cc_start: 0.6187 (tmm) cc_final: 0.5928 (tmm)
REVERT: D 1010 ASN cc_start: 0.8417 (t0) cc_final: 0.7813 (t0)
REVERT: C  905 TYR cc_start: 0.8809 (p90) cc_final: 0.8518 (p90)
REVERT: C  954 MET cc_start: 0.6011 (tmm) cc_final: 0.5716 (tmm)
REVERT: C 1010 ASN cc_start: 0.8474 (t0) cc_final: 0.7808 (t0)
REVERT: B   76 CYS cc_start: 0.7207 (t) cc_final: 0.6922 (p)
REVERT: B  297 LEU cc_start: 0.4643 (OUTLIER) cc_final: 0.4412 (pp)
REVERT: A   76 CYS cc_start: 0.7214 (t) cc_final: 0.6932 (p)
REVERT: A  297 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4384 (pp)
  outliers start: 16
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0732
  time to fit residues: 11.8551
Evaluate side-chains
  106 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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  892 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  237 GLN
Chi-restraints excluded: chain A residue  297 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0980
   chunk 52 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.156036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.125352 restraints weight = 10202.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.129215 restraints weight = 6065.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.131732 restraints weight = 4417.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.133356 restraints weight = 3614.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.134278 restraints weight = 3169.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6860  Z= 0.144
  Angle     :  0.775  11.584   9298  Z= 0.380
  Chirality :  0.044   0.203   1010
  Planarity :  0.005   0.063   1232
  Dihedral  :  5.606  25.130    958
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.75 %
    Favored  : 82.25 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 22.16 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.79 (0.25), residues: 862
  helix: -3.45 (0.42), residues: 96
  sheet: -2.20 (0.35), residues: 192
  loop : -3.74 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 861 
 TYR   0.009   0.001   TYR D 980 
 PHE   0.010   0.001   PHE D 840 
 TRP   0.005   0.001   TRP D 879 
 HIS   0.001   0.001   HIS D 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6858)
  covalent geometry    : angle       0.77444 ( 9294)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       1.32194 (    4)
  hydrogen bonds       : bond        0.02071 (   76)
  hydrogen bonds       : angle       5.17403 (  162)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1436.17 seconds
wall clock time: 25 minutes 28.91 seconds (1528.91 seconds total)