Starting phenix.real_space_refine
on Thu Jun  5 05:03:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qha_13968/06_2025/7qha_13968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qha_13968/06_2025/7qha_13968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qha_13968/06_2025/7qha_13968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qha_13968/06_2025/7qha_13968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qha_13968/06_2025/7qha_13968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qha_13968/06_2025/7qha_13968.cif"
  }
  resolution = 2.97
  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=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     Na      2      4.78       5
     C    3506      2.51       5
     N     832      2.21       5
     O     909      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5282
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1257
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 4, 'TRANS': 148}
    Chain: "B"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3208
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 404}
    Chain: "C"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 815
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 4, 'TRANS': 99}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' NA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.60, per 1000 atoms: 0.87
  Number of scatterers: 5282
  At special positions: 0
  Unit cell: (88.8769, 77.2481, 98.0138, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     Na      2     11.00
     O     909      8.00
     N     832      7.00
     C    3506      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.04

  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: 3.19
  Conformation dependent library (CDL) restraints added in 945.7 milliseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1248

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      71.3% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 8 through 34
      Proline residue:  A  16  - end of helix
      removed outlier: 3.510A  pdb=" N   ARG A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 64
      removed outlier: 4.150A  pdb=" N   ALA A  59 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ILE A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
    Processing helix  chain 'A' and resid 78 through 111
    Processing helix  chain 'A' and resid 123 through 128
    Processing helix  chain 'A' and resid 128 through 152
      removed outlier: 3.553A  pdb=" N   PHE A 136 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 15
    Processing helix  chain 'B' and resid 17 through 33
    Processing helix  chain 'B' and resid 37 through 47
      removed outlier: 4.449A  pdb=" N   ALA B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   GLN B  43 " --> pdb=" O   ASN B  39 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY B  47 " --> pdb=" O   GLN B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'B' and resid 55 through 70
      removed outlier: 4.097A  pdb=" N   PHE B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   ASN B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER B  69 " --> pdb=" O   HIS B  65 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 85
    Processing helix  chain 'B' and resid 90 through 103
      removed outlier: 4.129A  pdb=" N   VAL B  94 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   SER B  99 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.517A  pdb=" N   ASP B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLN B 118 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   LEU B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ASP B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 142 through 145
    Processing helix  chain 'B' and resid 151 through 162
    Processing helix  chain 'B' and resid 164 through 172
      removed outlier: 3.588A  pdb=" N   LEU B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 195
      removed outlier: 4.069A  pdb=" N   GLY B 176 " --> pdb=" O   GLY B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 214
    Processing helix  chain 'B' and resid 218 through 230
      removed outlier: 4.369A  pdb=" N   PHE B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B 230 " --> pdb=" O   GLY B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 250
    Processing helix  chain 'B' and resid 258 through 294
    Processing helix  chain 'B' and resid 295 through 307
      removed outlier: 3.999A  pdb=" N   ILE B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 325
      removed outlier: 3.580A  pdb=" N   LEU B 313 " --> pdb=" O   ASN B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 337
    Processing helix  chain 'B' and resid 337 through 347
      Proline residue:  B 343  - end of helix
    Processing helix  chain 'B' and resid 351 through 367
      removed outlier: 3.503A  pdb=" N   PHE B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 384
    Processing helix  chain 'B' and resid 389 through 395
    Processing helix  chain 'B' and resid 398 through 411
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 103 through 107
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116
      removed outlier: 3.814A  pdb=" N   ILE A 121 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 18 through 22
      removed outlier: 3.675A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59
      removed outlier: 7.033A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   GLY C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   MET C  34 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    1014 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: 1.46

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1596
        1.35 -     1.46: 1294
        1.46 -     1.58: 2458
        1.58 -     1.70: 0
        1.70 -     1.81: 57
  Bond restraints: 5405
  Sorted by residual:
  bond pdb=" CB  ASN C  76 "
       pdb=" CG  ASN C  76 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.27e+00
  bond pdb=" CB  ASP B 112 "
       pdb=" CG  ASP B 112 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.63e-01
  bond pdb=" C   SER B  90 "
       pdb=" O   SER B  90 "
    ideal  model  delta    sigma   weight residual
    1.243  1.234  0.009 9.50e-03 1.11e+04 9.29e-01
  bond pdb=" CB  ASP C  30 "
       pdb=" CG  ASP C  30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.68e-01
  bond pdb=" CB  GLU B 301 "
       pdb=" CG  GLU B 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.86e-01
  ... (remaining 5400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 7235
        1.95 -     3.90: 94
        3.90 -     5.85: 15
        5.85 -     7.79: 7
        7.79 -     9.74: 1
  Bond angle restraints: 7352
  Sorted by residual:
  angle pdb=" C   SER B  90 "
        pdb=" CA  SER B  90 "
        pdb=" CB  SER B  90 "
      ideal   model   delta    sigma   weight residual
     117.23  110.33    6.90 1.36e+00 5.41e-01 2.58e+01
  angle pdb=" C   SER B 151 "
        pdb=" N   ILE B 152 "
        pdb=" CA  ILE B 152 "
      ideal   model   delta    sigma   weight residual
     120.33  123.22   -2.89 8.00e-01 1.56e+00 1.31e+01
  angle pdb=" CA  SER B  90 "
        pdb=" C   SER B  90 "
        pdb=" N   LEU B  91 "
      ideal   model   delta    sigma   weight residual
     119.98  116.95    3.03 8.50e-01 1.38e+00 1.27e+01
  angle pdb=" C   LYS A  64 "
        pdb=" N   ASP A  65 "
        pdb=" CA  ASP A  65 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.48e+00
  angle pdb=" CA  LEU B 421 "
        pdb=" CB  LEU B 421 "
        pdb=" CG  LEU B 421 "
      ideal   model   delta    sigma   weight residual
     116.30  126.04   -9.74 3.50e+00 8.16e-02 7.75e+00
  ... (remaining 7347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 2911
       16.57 -    33.15: 192
       33.15 -    49.72: 42
       49.72 -    66.30: 7
       66.30 -    82.87: 3
  Dihedral angle restraints: 3155
    sinusoidal: 1199
      harmonic: 1956
  Sorted by residual:
  dihedral pdb=" CA  ASP C 103 "
           pdb=" CB  ASP C 103 "
           pdb=" CG  ASP C 103 "
           pdb=" OD1 ASP C 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.00   58.00     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  TYR C  94 "
           pdb=" C   TYR C  94 "
           pdb=" N   CYS C  95 "
           pdb=" CA  CYS C  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.60  -16.40     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ILE B 228 "
           pdb=" C   ILE B 228 "
           pdb=" N   PHE B 229 "
           pdb=" CA  PHE B 229 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.65  -15.35     0      5.00e+00 4.00e-02 9.42e+00
  ... (remaining 3152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 623
       0.039 -    0.078: 200
       0.078 -    0.117: 47
       0.117 -    0.155: 8
       0.155 -    0.194: 2
  Chirality restraints: 880
  Sorted by residual:
  chirality pdb=" CA  THR B 220 "
            pdb=" N   THR B 220 "
            pdb=" C   THR B 220 "
            pdb=" CB  THR B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.44e-01
  chirality pdb=" CA  VAL B 399 "
            pdb=" N   VAL B 399 "
            pdb=" C   VAL B 399 "
            pdb=" CB  VAL B 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.29    0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CB  THR B 220 "
            pdb=" CA  THR B 220 "
            pdb=" OG1 THR B 220 "
            pdb=" CG2 THR B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 877 not shown)

  Planarity restraints: 897
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  76 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.53e+00
        pdb=" C   ASN C  76 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ASN C  76 "    0.013 2.00e-02 2.50e+03
        pdb=" N   THR C  77 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 145 "   -0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B 146 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 146 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 146 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 309 "   -0.019 5.00e-02 4.00e+02   2.90e-02 1.34e+00
        pdb=" N   PRO B 310 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 310 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 310 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 894 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1295
        2.79 -     3.32: 5415
        3.32 -     3.85: 8530
        3.85 -     4.37: 8948
        4.37 -     4.90: 16317
  Nonbonded interactions: 40505
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  25 "
            pdb=" OD1 ASN C  76 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU B 302 "
            pdb=" OG  SER B 305 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   TYR C  98 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   SER B 103 "
            pdb="NA    NA B 501 "
     model   vdw
     2.312 2.470
  nonbonded pdb=" OG  SER B 380 "
            pdb=" O   ILE B 385 "
     model   vdw
     2.316 3.040
  ... (remaining 40500 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             19.180
  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:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.680
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:16.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5406  Z= 0.126
  Angle     :  0.592   9.742   7354  Z= 0.311
  Chirality :  0.041   0.194    880
  Planarity :  0.004   0.031    897
  Dihedral  : 12.232  82.871   1904
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.33), residues: 678
  helix:  2.20 (0.25), residues: 428
  sheet: -0.36 (0.97), residues: 35
  loop : -0.50 (0.43), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 388 
 PHE   0.019   0.001   PHE B  60 
 TYR   0.013   0.001   TYR B 129 
 ARG   0.001   0.000   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15164 (  349)
  hydrogen bonds       : angle       5.84232 ( 1014)
  SS BOND              : bond        0.00522 (    1)
  SS BOND              : angle       1.29784 (    2)
  covalent geometry    : bond        0.00264 ( 5405)
  covalent geometry    : angle       0.59128 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8801 (ttm) cc_final: 0.8601 (ttm)
REVERT: A   71 THR cc_start: 0.8147 (t) cc_final: 0.7545 (t)
REVERT: A   75 ASP cc_start: 0.9189 (m-30) cc_final: 0.8825 (m-30)
REVERT: B  118 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8548 (tm-30)
REVERT: B  130 ASP cc_start: 0.8576 (t70) cc_final: 0.8205 (t0)
REVERT: B  351 ASP cc_start: 0.8909 (p0) cc_final: 0.8662 (p0)
REVERT: C   61 ASP cc_start: 0.8595 (t70) cc_final: 0.8350 (t0)
REVERT: C   85 LEU cc_start: 0.8950 (mm) cc_final: 0.8664 (mm)
  outliers start: 0
  outliers final: 1
  residues processed: 137
  average time/residue: 1.3508
  time to fit residues: 194.7422
Evaluate side-chains
  105 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0010
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  95 ASN
B 384 ASN
C  81 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.070718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.058554 restraints weight = 13863.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 3.66
r_work: 0.2687 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5406  Z= 0.137
  Angle     :  0.646  12.280   7354  Z= 0.320
  Chirality :  0.041   0.190    880
  Planarity :  0.005   0.035    897
  Dihedral  :  4.043  22.985    734
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.04 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.34), residues: 678
  helix:  2.34 (0.25), residues: 440
  sheet: -0.17 (0.96), residues: 35
  loop : -0.60 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 
 PHE   0.014   0.001   PHE B  60 
 TYR   0.016   0.001   TYR B 425 
 ARG   0.007   0.001   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  349)
  hydrogen bonds       : angle       4.23957 ( 1014)
  SS BOND              : bond        0.00493 (    1)
  SS BOND              : angle       1.61166 (    2)
  covalent geometry    : bond        0.00296 ( 5405)
  covalent geometry    : angle       0.64596 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.9004 (tpp) cc_final: 0.8702 (tpp)
REVERT: A   71 THR cc_start: 0.8367 (t) cc_final: 0.7876 (t)
REVERT: A   75 ASP cc_start: 0.9294 (m-30) cc_final: 0.9002 (m-30)
REVERT: B  118 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8524 (tm-30)
REVERT: B  130 ASP cc_start: 0.8265 (t70) cc_final: 0.7791 (t0)
REVERT: B  351 ASP cc_start: 0.8962 (p0) cc_final: 0.8646 (p0)
REVERT: B  372 MET cc_start: 0.7887 (tpp) cc_final: 0.7230 (tmm)
REVERT: B  418 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8936 (tm)
REVERT: C   46 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7110 (tm-30)
REVERT: C   85 LEU cc_start: 0.9114 (mm) cc_final: 0.8802 (mm)
REVERT: C  108 TRP cc_start: 0.7855 (m-10) cc_final: 0.7141 (m-10)
  outliers start: 15
  outliers final: 4
  residues processed: 121
  average time/residue: 1.0342
  time to fit residues: 131.2504
Evaluate side-chains
  110 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
B  93 HIS
B 384 ASN
C  81 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.070730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.058418 restraints weight = 14066.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 3.67
r_work: 0.2691 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5406  Z= 0.136
  Angle     :  0.637  11.416   7354  Z= 0.314
  Chirality :  0.041   0.186    880
  Planarity :  0.005   0.034    897
  Dihedral  :  3.924  21.061    732
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.42 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.33), residues: 678
  helix:  2.42 (0.25), residues: 437
  sheet: -0.39 (0.91), residues: 35
  loop : -0.54 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 108 
 HIS   0.005   0.001   HIS B 354 
 PHE   0.019   0.001   PHE B 340 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.009   0.001   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  349)
  hydrogen bonds       : angle       3.96226 ( 1014)
  SS BOND              : bond        0.00679 (    1)
  SS BOND              : angle       2.18892 (    2)
  covalent geometry    : bond        0.00305 ( 5405)
  covalent geometry    : angle       0.63583 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ASN cc_start: 0.7948 (m-40) cc_final: 0.7616 (m110)
REVERT: A   11 GLU cc_start: 0.8594 (pm20) cc_final: 0.8380 (pm20)
REVERT: A   71 THR cc_start: 0.8403 (t) cc_final: 0.7903 (t)
REVERT: A   75 ASP cc_start: 0.9314 (m-30) cc_final: 0.9013 (m-30)
REVERT: B  118 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: B  120 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8943 (mt-10)
REVERT: B  130 ASP cc_start: 0.8343 (t70) cc_final: 0.7638 (t0)
REVERT: B  331 LEU cc_start: 0.9174 (tp) cc_final: 0.8927 (tm)
REVERT: B  351 ASP cc_start: 0.9008 (p0) cc_final: 0.8700 (p0)
REVERT: B  418 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8996 (tm)
REVERT: C   46 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7147 (tm-30)
REVERT: C   82 MET cc_start: 0.8913 (mpp) cc_final: 0.8547 (mpp)
REVERT: C   85 LEU cc_start: 0.9112 (mm) cc_final: 0.8735 (mm)
REVERT: C  108 TRP cc_start: 0.8057 (m-10) cc_final: 0.7848 (m-10)
  outliers start: 21
  outliers final: 7
  residues processed: 120
  average time/residue: 1.2265
  time to fit residues: 155.0115
Evaluate side-chains
  110 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.066660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.054298 restraints weight = 14673.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 3.71
r_work: 0.2596 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5406  Z= 0.222
  Angle     :  0.704  11.455   7354  Z= 0.347
  Chirality :  0.043   0.151    880
  Planarity :  0.005   0.034    897
  Dihedral  :  4.116  22.531    732
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.82 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.33), residues: 678
  helix:  2.40 (0.25), residues: 435
  sheet: -0.34 (0.93), residues: 35
  loop : -0.63 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 108 
 HIS   0.005   0.001   HIS B 354 
 PHE   0.010   0.001   PHE B  59 
 TYR   0.011   0.001   TYR C  94 
 ARG   0.006   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05387 (  349)
  hydrogen bonds       : angle       4.14094 ( 1014)
  SS BOND              : bond        0.00661 (    1)
  SS BOND              : angle       2.03681 (    2)
  covalent geometry    : bond        0.00526 ( 5405)
  covalent geometry    : angle       0.70313 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8610 (pm20) cc_final: 0.8270 (pm20)
REVERT: A   66 ASP cc_start: 0.9118 (m-30) cc_final: 0.8824 (m-30)
REVERT: A   71 THR cc_start: 0.8556 (t) cc_final: 0.8072 (t)
REVERT: A   75 ASP cc_start: 0.9334 (m-30) cc_final: 0.9049 (m-30)
REVERT: B  118 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8793 (tm-30)
REVERT: B  130 ASP cc_start: 0.8347 (t70) cc_final: 0.7612 (t0)
REVERT: B  197 MET cc_start: 0.8306 (ppp) cc_final: 0.8066 (ppp)
REVERT: B  259 MET cc_start: 0.8446 (pmm) cc_final: 0.8157 (pmm)
REVERT: B  268 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8871 (mm-30)
REVERT: B  294 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7989 (tp40)
REVERT: B  331 LEU cc_start: 0.9227 (tp) cc_final: 0.8978 (tm)
REVERT: B  351 ASP cc_start: 0.8992 (p0) cc_final: 0.8691 (p0)
REVERT: B  384 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8892 (t0)
REVERT: B  418 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9005 (tm)
REVERT: C   46 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7038 (tm-30)
REVERT: C   82 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8605 (mpp)
REVERT: C   85 LEU cc_start: 0.9196 (mm) cc_final: 0.8842 (mm)
REVERT: C  102 ASP cc_start: 0.8869 (t0) cc_final: 0.8459 (t0)
REVERT: C  108 TRP cc_start: 0.8155 (m-10) cc_final: 0.7935 (m-10)
  outliers start: 25
  outliers final: 12
  residues processed: 120
  average time/residue: 0.9589
  time to fit residues: 121.0929
Evaluate side-chains
  118 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  384 ASN
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.067802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.055593 restraints weight = 14296.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 3.63
r_work: 0.2627 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5406  Z= 0.157
  Angle     :  0.685  11.206   7354  Z= 0.334
  Chirality :  0.041   0.157    880
  Planarity :  0.004   0.037    897
  Dihedral  :  4.087  22.270    732
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.75 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.33), residues: 678
  helix:  2.39 (0.25), residues: 436
  sheet: -0.47 (0.93), residues: 35
  loop : -0.65 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.005   0.001   HIS B 354 
 PHE   0.008   0.001   PHE B  59 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.009   0.001   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04994 (  349)
  hydrogen bonds       : angle       3.98383 ( 1014)
  SS BOND              : bond        0.00700 (    1)
  SS BOND              : angle       1.74204 (    2)
  covalent geometry    : bond        0.00367 ( 5405)
  covalent geometry    : angle       0.68484 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ASN cc_start: 0.8028 (m-40) cc_final: 0.7679 (m110)
REVERT: A   11 GLU cc_start: 0.8594 (pm20) cc_final: 0.8273 (pm20)
REVERT: A   66 ASP cc_start: 0.9111 (m-30) cc_final: 0.8829 (m-30)
REVERT: A   71 THR cc_start: 0.8523 (t) cc_final: 0.8039 (t)
REVERT: A   75 ASP cc_start: 0.9328 (m-30) cc_final: 0.9042 (m-30)
REVERT: B  118 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8792 (tm-30)
REVERT: B  130 ASP cc_start: 0.8366 (t70) cc_final: 0.7601 (t0)
REVERT: B  197 MET cc_start: 0.8363 (ppp) cc_final: 0.8109 (ppp)
REVERT: B  331 LEU cc_start: 0.9217 (tp) cc_final: 0.8997 (tm)
REVERT: B  351 ASP cc_start: 0.9040 (p0) cc_final: 0.8761 (p0)
REVERT: B  384 ASN cc_start: 0.9108 (t0) cc_final: 0.8880 (t0)
REVERT: B  418 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8996 (tm)
REVERT: C   34 MET cc_start: 0.8236 (tmm) cc_final: 0.8026 (tmm)
REVERT: C   46 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7096 (tm-30)
REVERT: C   82 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8659 (mpp)
REVERT: C   85 LEU cc_start: 0.9204 (mm) cc_final: 0.8855 (mm)
REVERT: C  108 TRP cc_start: 0.8145 (m-10) cc_final: 0.7932 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 118
  average time/residue: 0.9657
  time to fit residues: 120.2867
Evaluate side-chains
  117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.067161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.054945 restraints weight = 14405.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 3.57
r_work: 0.2614 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5406  Z= 0.189
  Angle     :  0.705  11.170   7354  Z= 0.345
  Chirality :  0.043   0.163    880
  Planarity :  0.004   0.033    897
  Dihedral  :  4.159  22.564    732
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.33 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.33), residues: 678
  helix:  2.41 (0.25), residues: 436
  sheet: -0.57 (0.94), residues: 35
  loop : -0.65 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.005   0.001   HIS B 354 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.007   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05187 (  349)
  hydrogen bonds       : angle       4.05231 ( 1014)
  SS BOND              : bond        0.00663 (    1)
  SS BOND              : angle       1.76326 (    2)
  covalent geometry    : bond        0.00447 ( 5405)
  covalent geometry    : angle       0.70413 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8656 (pm20) cc_final: 0.8222 (pm20)
REVERT: A   43 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6894 (tm-30)
REVERT: A   71 THR cc_start: 0.8609 (t) cc_final: 0.8113 (t)
REVERT: A   75 ASP cc_start: 0.9344 (m-30) cc_final: 0.9061 (m-30)
REVERT: B  118 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8830 (tm-30)
REVERT: B  130 ASP cc_start: 0.8412 (t70) cc_final: 0.7612 (t0)
REVERT: B  197 MET cc_start: 0.8447 (ppp) cc_final: 0.8106 (ppp)
REVERT: B  259 MET cc_start: 0.8452 (pmm) cc_final: 0.8230 (pmm)
REVERT: B  268 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8846 (mm-30)
REVERT: B  294 GLN cc_start: 0.8171 (tp40) cc_final: 0.7941 (tp-100)
REVERT: B  331 LEU cc_start: 0.9265 (tp) cc_final: 0.9050 (tm)
REVERT: B  351 ASP cc_start: 0.9024 (p0) cc_final: 0.8736 (p0)
REVERT: B  372 MET cc_start: 0.8199 (tpp) cc_final: 0.7459 (tmm)
REVERT: B  384 ASN cc_start: 0.9179 (t0) cc_final: 0.8902 (t0)
REVERT: B  418 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9008 (tm)
REVERT: C   46 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7168 (tm-30)
REVERT: C   82 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8715 (mpp)
REVERT: C   85 LEU cc_start: 0.9252 (mm) cc_final: 0.8907 (mm)
REVERT: C  102 ASP cc_start: 0.8780 (t0) cc_final: 0.8433 (t0)
REVERT: C  108 TRP cc_start: 0.8248 (m-10) cc_final: 0.7971 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 120
  average time/residue: 0.9573
  time to fit residues: 120.8409
Evaluate side-chains
  121 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0980
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.068264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.056098 restraints weight = 14127.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 3.67
r_work: 0.2635 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5406  Z= 0.149
  Angle     :  0.713  12.971   7354  Z= 0.345
  Chirality :  0.041   0.150    880
  Planarity :  0.004   0.032    897
  Dihedral  :  4.055  21.844    732
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.56 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.33), residues: 678
  helix:  2.45 (0.25), residues: 436
  sheet: -0.55 (0.96), residues: 35
  loop : -0.67 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 354 
 PHE   0.008   0.001   PHE B  59 
 TYR   0.010   0.001   TYR A 103 
 ARG   0.008   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04668 (  349)
  hydrogen bonds       : angle       3.90372 ( 1014)
  SS BOND              : bond        0.00604 (    1)
  SS BOND              : angle       1.66805 (    2)
  covalent geometry    : bond        0.00349 ( 5405)
  covalent geometry    : angle       0.71239 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8614 (pm20) cc_final: 0.8242 (pm20)
REVERT: A   66 ASP cc_start: 0.9059 (m-30) cc_final: 0.8762 (m-30)
REVERT: A   71 THR cc_start: 0.8514 (t) cc_final: 0.8013 (t)
REVERT: A   75 ASP cc_start: 0.9335 (m-30) cc_final: 0.9057 (m-30)
REVERT: B  118 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8801 (tm-30)
REVERT: B  129 TYR cc_start: 0.8793 (m-10) cc_final: 0.8581 (m-10)
REVERT: B  130 ASP cc_start: 0.8355 (t70) cc_final: 0.7530 (t0)
REVERT: B  197 MET cc_start: 0.8466 (ppp) cc_final: 0.8192 (ppp)
REVERT: B  268 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8836 (mm-30)
REVERT: B  279 MET cc_start: 0.8999 (tpp) cc_final: 0.8744 (tpp)
REVERT: B  331 LEU cc_start: 0.9209 (tp) cc_final: 0.8985 (tm)
REVERT: B  351 ASP cc_start: 0.9040 (p0) cc_final: 0.8742 (p0)
REVERT: B  372 MET cc_start: 0.8268 (tpp) cc_final: 0.7550 (tmm)
REVERT: B  384 ASN cc_start: 0.9111 (t0) cc_final: 0.8798 (t0)
REVERT: B  418 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8971 (tm)
REVERT: C   34 MET cc_start: 0.8248 (tmm) cc_final: 0.8043 (tmm)
REVERT: C   46 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7029 (tm-30)
REVERT: C   82 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8667 (mpp)
REVERT: C   85 LEU cc_start: 0.9220 (mm) cc_final: 0.8874 (mm)
REVERT: C  102 ASP cc_start: 0.8781 (t0) cc_final: 0.8450 (t0)
REVERT: C  108 TRP cc_start: 0.8223 (m-10) cc_final: 0.7988 (m-10)
  outliers start: 18
  outliers final: 13
  residues processed: 122
  average time/residue: 0.9549
  time to fit residues: 123.5641
Evaluate side-chains
  120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.069309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.057104 restraints weight = 14265.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 3.67
r_work: 0.2656 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5406  Z= 0.143
  Angle     :  0.727  12.267   7354  Z= 0.349
  Chirality :  0.041   0.141    880
  Planarity :  0.004   0.032    897
  Dihedral  :  4.022  21.516    732
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.39 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.33), residues: 678
  helix:  2.40 (0.25), residues: 434
  sheet: -0.59 (0.96), residues: 35
  loop : -0.61 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 
 PHE   0.007   0.001   PHE B  59 
 TYR   0.012   0.001   TYR B 425 
 ARG   0.008   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04505 (  349)
  hydrogen bonds       : angle       3.86850 ( 1014)
  SS BOND              : bond        0.00596 (    1)
  SS BOND              : angle       1.54162 (    2)
  covalent geometry    : bond        0.00327 ( 5405)
  covalent geometry    : angle       0.72648 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8615 (pm20) cc_final: 0.8242 (pm20)
REVERT: A   66 ASP cc_start: 0.9082 (m-30) cc_final: 0.8785 (m-30)
REVERT: A   71 THR cc_start: 0.8508 (t) cc_final: 0.8007 (t)
REVERT: A   75 ASP cc_start: 0.9345 (m-30) cc_final: 0.9064 (m-30)
REVERT: B  130 ASP cc_start: 0.8362 (t70) cc_final: 0.7503 (t0)
REVERT: B  206 GLU cc_start: 0.8683 (pm20) cc_final: 0.8370 (pm20)
REVERT: B  268 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8851 (mm-30)
REVERT: B  351 ASP cc_start: 0.9052 (p0) cc_final: 0.8753 (p0)
REVERT: B  372 MET cc_start: 0.8329 (tpp) cc_final: 0.7622 (tmm)
REVERT: B  384 ASN cc_start: 0.9105 (t0) cc_final: 0.8811 (t0)
REVERT: B  418 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9001 (tm)
REVERT: C   46 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7030 (tm-30)
REVERT: C   82 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8683 (mpp)
REVERT: C   85 LEU cc_start: 0.9203 (mm) cc_final: 0.8858 (mm)
REVERT: C  108 TRP cc_start: 0.8249 (m-10) cc_final: 0.7244 (m-10)
  outliers start: 21
  outliers final: 16
  residues processed: 121
  average time/residue: 1.0164
  time to fit residues: 129.5002
Evaluate side-chains
  122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0470
   chunk 66 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.6084

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
C  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.067879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.055562 restraints weight = 14169.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 3.67
r_work: 0.2627 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5406  Z= 0.174
  Angle     :  0.804  14.960   7354  Z= 0.378
  Chirality :  0.042   0.148    880
  Planarity :  0.004   0.033    897
  Dihedral  :  4.089  21.634    732
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 25.61 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.33), residues: 678
  helix:  2.35 (0.25), residues: 436
  sheet: -0.69 (0.95), residues: 35
  loop : -0.63 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 354 
 PHE   0.008   0.001   PHE B  59 
 TYR   0.010   0.001   TYR B 196 
 ARG   0.008   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04803 (  349)
  hydrogen bonds       : angle       3.94621 ( 1014)
  SS BOND              : bond        0.00527 (    1)
  SS BOND              : angle       1.71681 (    2)
  covalent geometry    : bond        0.00412 ( 5405)
  covalent geometry    : angle       0.80316 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8633 (pm20) cc_final: 0.8238 (pm20)
REVERT: A   66 ASP cc_start: 0.9089 (m-30) cc_final: 0.8788 (m-30)
REVERT: A   71 THR cc_start: 0.8540 (t) cc_final: 0.8034 (t)
REVERT: A   75 ASP cc_start: 0.9345 (m-30) cc_final: 0.9068 (m-30)
REVERT: B  130 ASP cc_start: 0.8300 (t70) cc_final: 0.7406 (t0)
REVERT: B  206 GLU cc_start: 0.8675 (pm20) cc_final: 0.8362 (pm20)
REVERT: B  268 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8868 (mm-30)
REVERT: B  294 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8185 (tp40)
REVERT: B  351 ASP cc_start: 0.9032 (p0) cc_final: 0.8753 (p0)
REVERT: B  372 MET cc_start: 0.8402 (tpp) cc_final: 0.7657 (tmm)
REVERT: B  384 ASN cc_start: 0.9143 (t0) cc_final: 0.8858 (t0)
REVERT: B  418 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9012 (tm)
REVERT: C   46 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7103 (tm-30)
REVERT: C   82 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (mpp)
REVERT: C   85 LEU cc_start: 0.9226 (mm) cc_final: 0.8872 (mm)
REVERT: C  102 ASP cc_start: 0.8754 (t0) cc_final: 0.8409 (t0)
REVERT: C  108 TRP cc_start: 0.8285 (m-10) cc_final: 0.8001 (m-10)
  outliers start: 22
  outliers final: 16
  residues processed: 123
  average time/residue: 0.9123
  time to fit residues: 118.4614
Evaluate side-chains
  125 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.069792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.057591 restraints weight = 14299.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 3.68
r_work: 0.2668 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5406  Z= 0.146
  Angle     :  0.762  12.245   7354  Z= 0.367
  Chirality :  0.041   0.153    880
  Planarity :  0.004   0.033    897
  Dihedral  :  4.037  21.727    732
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 26.67 %
    Favored  : 69.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.33), residues: 678
  helix:  2.36 (0.25), residues: 434
  sheet: -0.74 (0.97), residues: 35
  loop : -0.65 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 
 PHE   0.009   0.001   PHE B 229 
 TYR   0.009   0.001   TYR A 103 
 ARG   0.008   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  349)
  hydrogen bonds       : angle       3.88928 ( 1014)
  SS BOND              : bond        0.00577 (    1)
  SS BOND              : angle       1.63586 (    2)
  covalent geometry    : bond        0.00335 ( 5405)
  covalent geometry    : angle       0.76125 ( 7352)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8586 (pm20) cc_final: 0.8208 (pm20)
REVERT: A   66 ASP cc_start: 0.9099 (m-30) cc_final: 0.8823 (m-30)
REVERT: A   71 THR cc_start: 0.8484 (t) cc_final: 0.7975 (t)
REVERT: A   75 ASP cc_start: 0.9323 (m-30) cc_final: 0.9036 (m-30)
REVERT: B  129 TYR cc_start: 0.9003 (m-10) cc_final: 0.8697 (m-10)
REVERT: B  130 ASP cc_start: 0.8249 (t70) cc_final: 0.7314 (t0)
REVERT: B  197 MET cc_start: 0.8647 (pp-130) cc_final: 0.8427 (ppp)
REVERT: B  206 GLU cc_start: 0.8683 (pm20) cc_final: 0.8377 (pm20)
REVERT: B  268 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8830 (mm-30)
REVERT: B  294 GLN cc_start: 0.8451 (tp-100) cc_final: 0.8207 (tp40)
REVERT: B  351 ASP cc_start: 0.9049 (p0) cc_final: 0.8746 (p0)
REVERT: B  372 MET cc_start: 0.8439 (tpp) cc_final: 0.7742 (tmm)
REVERT: B  384 ASN cc_start: 0.9087 (t0) cc_final: 0.8831 (t0)
REVERT: B  418 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9035 (tm)
REVERT: C   46 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7037 (tm-30)
REVERT: C   82 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8472 (mpm)
REVERT: C   85 LEU cc_start: 0.9204 (mm) cc_final: 0.8818 (mm)
  outliers start: 20
  outliers final: 13
  residues processed: 125
  average time/residue: 0.9198
  time to fit residues: 121.2789
Evaluate side-chains
  124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.069951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.057706 restraints weight = 14138.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 3.64
r_work: 0.2675 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5406  Z= 0.145
  Angle     :  0.781  12.307   7354  Z= 0.371
  Chirality :  0.042   0.173    880
  Planarity :  0.004   0.034    897
  Dihedral  :  3.973  20.856    732
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 27.72 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.33), residues: 678
  helix:  2.42 (0.25), residues: 435
  sheet: -0.81 (0.95), residues: 35
  loop : -0.67 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 
 PHE   0.015   0.001   PHE B 229 
 TYR   0.021   0.001   TYR B 425 
 ARG   0.008   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  349)
  hydrogen bonds       : angle       3.85621 ( 1014)
  SS BOND              : bond        0.00508 (    1)
  SS BOND              : angle       1.60935 (    2)
  covalent geometry    : bond        0.00334 ( 5405)
  covalent geometry    : angle       0.78056 ( 7352)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3903.38 seconds
wall clock time: 68 minutes 22.38 seconds (4102.38 seconds total)