Starting phenix.real_space_refine
on Tue Mar  3 13:31:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qha_13968/03_2026/7qha_13968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qha_13968/03_2026/7qha_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_13968/03_2026/7qha_13968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qha_13968/03_2026/7qha_13968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qha_13968/03_2026/7qha_13968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qha_13968/03_2026/7qha_13968.cif"
  }
  resolution = 2.97
  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=   0.011
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): 0.00s

  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: 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: 1.28, per 1000 atoms: 0.24
  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: 0.49
  Conformation dependent library (CDL) restraints added in 338.7 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: 0.16
  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: 0.87

  Time building geometry restraints manager: 0.65 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:             1.070
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.240
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:10.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.510
-------------------------------------------------------------------------------
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 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:  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
 ARG   0.001   0.000   ARG C  66 
 TYR   0.013   0.001   TYR B 129 
 PHE   0.019   0.001   PHE B  60 
 TRP   0.008   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 388 

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

*********************** 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  : 0.196 
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: 0.4393
  time to fit residues: 63.0974
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  : 0.187 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  93 HIS
B  95 ASN
B 384 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.071122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.058890 restraints weight = 14095.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.70
r_work: 0.2693 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1408

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     :  0.651  12.343   7354  Z= 0.322
  Chirality :  0.041   0.190    880
  Planarity :  0.005   0.035    897
  Dihedral  :  4.068  24.794    734
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.68 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.04 (0.34), residues: 678
  helix:  2.34 (0.25), residues: 440
  sheet: -0.15 (0.97), residues: 35
  loop : -0.60 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 207 
 TYR   0.017   0.001   TYR B 425 
 PHE   0.014   0.001   PHE B  60 
 TRP   0.024   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5405)
  covalent geometry    : angle       0.65072 ( 7352)
  SS BOND              : bond        0.00685 (    1)
  SS BOND              : angle       1.53430 (    2)
  hydrogen bonds       : bond        0.04632 (  349)
  hydrogen bonds       : angle       4.22181 ( 1014)

*********************** 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  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8962 (tpp) cc_final: 0.8701 (tpp)
REVERT: A   71 THR cc_start: 0.8361 (t) cc_final: 0.7873 (t)
REVERT: A   75 ASP cc_start: 0.9293 (m-30) cc_final: 0.8999 (m-30)
REVERT: A  128 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7757 (m-10)
REVERT: B  118 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8548 (tm-30)
REVERT: B  130 ASP cc_start: 0.8261 (t70) cc_final: 0.7784 (t0)
REVERT: B  351 ASP cc_start: 0.8979 (p0) cc_final: 0.8663 (p0)
REVERT: B  418 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8934 (tm)
REVERT: C   46 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7201 (tm-30)
REVERT: C   85 LEU cc_start: 0.9108 (mm) cc_final: 0.8782 (mm)
REVERT: C  108 TRP cc_start: 0.7904 (m-10) cc_final: 0.7194 (m-10)
  outliers start: 15
  outliers final: 4
  residues processed: 121
  average time/residue: 0.4712
  time to fit residues: 59.7163
Evaluate side-chains
  111 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
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  112 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.2786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.069877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.057602 restraints weight = 14090.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 3.65
r_work: 0.2674 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1695

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= 0.148
  Angle     :  0.643  11.397   7354  Z= 0.318
  Chirality :  0.041   0.186    880
  Planarity :  0.005   0.034    897
  Dihedral  :  3.937  21.644    732
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.05
  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 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:  2.14 (0.33), residues: 678
  helix:  2.44 (0.25), residues: 435
  sheet: -0.38 (0.91), residues: 35
  loop : -0.50 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 207 
 TYR   0.011   0.001   TYR A 128 
 PHE   0.020   0.001   PHE B 340 
 TRP   0.016   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5405)
  covalent geometry    : angle       0.64259 ( 7352)
  SS BOND              : bond        0.00655 (    1)
  SS BOND              : angle       1.87742 (    2)
  hydrogen bonds       : bond        0.04689 (  349)
  hydrogen bonds       : angle       4.00128 ( 1014)

*********************** 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
  131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ASN cc_start: 0.7974 (m-40) cc_final: 0.7559 (m110)
REVERT: A   11 GLU cc_start: 0.8570 (pm20) cc_final: 0.8315 (pm20)
REVERT: A   71 THR cc_start: 0.8435 (t) cc_final: 0.7938 (t)
REVERT: A   75 ASP cc_start: 0.9316 (m-30) cc_final: 0.9011 (m-30)
REVERT: B  118 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8718 (tm-30)
REVERT: B  120 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8934 (mt-10)
REVERT: B  130 ASP cc_start: 0.8334 (t70) cc_final: 0.7671 (t0)
REVERT: B  331 LEU cc_start: 0.9168 (tp) cc_final: 0.8918 (tm)
REVERT: B  351 ASP cc_start: 0.8994 (p0) cc_final: 0.8683 (p0)
REVERT: B  418 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8988 (tm)
REVERT: C   46 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7038 (tm-30)
REVERT: C   85 LEU cc_start: 0.9108 (mm) cc_final: 0.8772 (mm)
REVERT: C  108 TRP cc_start: 0.8039 (m-10) cc_final: 0.7820 (m-10)
  outliers start: 21
  outliers final: 7
  residues processed: 122
  average time/residue: 0.4349
  time to fit residues: 55.7516
Evaluate side-chains
  111 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  337 LEU
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 30 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3025 r_free = 0.3025 target = 0.068465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.056246 restraints weight = 14130.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 3.59
r_work: 0.2644 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2004

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= 0.172
  Angle     :  0.670  11.413   7354  Z= 0.328
  Chirality :  0.042   0.156    880
  Planarity :  0.004   0.034    897
  Dihedral  :  4.019  22.213    732
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.18 %
    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 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:  2.08 (0.33), residues: 678
  helix:  2.43 (0.25), residues: 435
  sheet: -0.51 (0.93), residues: 35
  loop : -0.59 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 392 
 TYR   0.010   0.001   TYR C  94 
 PHE   0.010   0.001   PHE B  60 
 TRP   0.013   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5405)
  covalent geometry    : angle       0.66964 ( 7352)
  SS BOND              : bond        0.00617 (    1)
  SS BOND              : angle       1.83599 (    2)
  hydrogen bonds       : bond        0.04932 (  349)
  hydrogen bonds       : angle       4.00921 ( 1014)

*********************** 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: 23
    poor density    : 108
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8625 (pm20) cc_final: 0.8289 (pm20)
REVERT: A   66 ASP cc_start: 0.9114 (m-30) cc_final: 0.8817 (m-30)
REVERT: A   71 THR cc_start: 0.8529 (t) cc_final: 0.8026 (t)
REVERT: A   75 ASP cc_start: 0.9318 (m-30) cc_final: 0.9017 (m-30)
REVERT: B  130 ASP cc_start: 0.8352 (t70) cc_final: 0.7591 (t0)
REVERT: B  197 MET cc_start: 0.8289 (ppp) cc_final: 0.8064 (ppp)
REVERT: B  268 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8829 (mm-30)
REVERT: B  294 GLN cc_start: 0.8302 (tp-100) cc_final: 0.8017 (tp40)
REVERT: B  331 LEU cc_start: 0.9244 (tp) cc_final: 0.8994 (tm)
REVERT: B  351 ASP cc_start: 0.9003 (p0) cc_final: 0.8701 (p0)
REVERT: B  384 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8823 (t0)
REVERT: B  418 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9024 (tm)
REVERT: C   46 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7097 (tm-30)
REVERT: C   82 MET cc_start: 0.8974 (mpt) cc_final: 0.8745 (mpp)
REVERT: C   85 LEU cc_start: 0.9144 (mm) cc_final: 0.8830 (mm)
  outliers start: 23
  outliers final: 11
  residues processed: 121
  average time/residue: 0.4481
  time to fit residues: 56.8486
Evaluate side-chains
  116 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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  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  112 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0270
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3069 r_free = 0.3069 target = 0.070814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.058454 restraints weight = 14255.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 3.60
r_work: 0.2690 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5406  Z= 0.133
  Angle     :  0.670  11.109   7354  Z= 0.326
  Chirality :  0.040   0.186    880
  Planarity :  0.004   0.033    897
  Dihedral  :  3.941  21.189    732
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.58 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.92 (0.33), residues: 678
  helix:  2.32 (0.25), residues: 442
  sheet: -0.67 (0.93), residues: 35
  loop : -0.80 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  47 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.007   0.001   PHE B  60 
 TRP   0.013   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5405)
  covalent geometry    : angle       0.66972 ( 7352)
  SS BOND              : bond        0.00657 (    1)
  SS BOND              : angle       1.59340 (    2)
  hydrogen bonds       : bond        0.04369 (  349)
  hydrogen bonds       : angle       3.86003 ( 1014)

*********************** 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
  128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8594 (pm20) cc_final: 0.8293 (pm20)
REVERT: A   71 THR cc_start: 0.8452 (t) cc_final: 0.7949 (t)
REVERT: A   75 ASP cc_start: 0.9295 (m-30) cc_final: 0.8994 (m-30)
REVERT: B  130 ASP cc_start: 0.8388 (t70) cc_final: 0.7568 (t0)
REVERT: B  197 MET cc_start: 0.8356 (ppp) cc_final: 0.8118 (ppp)
REVERT: B  268 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8827 (mm-30)
REVERT: B  331 LEU cc_start: 0.9220 (tp) cc_final: 0.9012 (tm)
REVERT: B  351 ASP cc_start: 0.9042 (p0) cc_final: 0.8755 (p0)
REVERT: B  418 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8994 (tm)
REVERT: C   46 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7092 (tm-30)
REVERT: C   82 MET cc_start: 0.8949 (mpt) cc_final: 0.8473 (mpm)
REVERT: C   85 LEU cc_start: 0.9104 (mm) cc_final: 0.8749 (mm)
REVERT: C  108 TRP cc_start: 0.8003 (m-10) cc_final: 0.7172 (m-10)
  outliers start: 18
  outliers final: 9
  residues processed: 121
  average time/residue: 0.4352
  time to fit residues: 55.2655
Evaluate side-chains
  116 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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  303 PHE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 3 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN
C  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.067979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.055832 restraints weight = 14306.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2763 rms_B_bonded: 3.62
r_work: 0.2632 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5406  Z= 0.171
  Angle     :  0.713  11.108   7354  Z= 0.345
  Chirality :  0.042   0.156    880
  Planarity :  0.004   0.033    897
  Dihedral  :  4.012  20.856    732
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.16 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.08 (0.33), residues: 678
  helix:  2.45 (0.25), residues: 436
  sheet: -0.73 (0.95), residues: 35
  loop : -0.60 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 392 
 TYR   0.010   0.001   TYR C  94 
 PHE   0.019   0.001   PHE B 229 
 TRP   0.014   0.001   TRP C 108 
 HIS   0.004   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5405)
  covalent geometry    : angle       0.71273 ( 7352)
  SS BOND              : bond        0.00540 (    1)
  SS BOND              : angle       1.69737 (    2)
  hydrogen bonds       : bond        0.04786 (  349)
  hydrogen bonds       : angle       3.92201 ( 1014)

*********************** 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
  128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8621 (pm20) cc_final: 0.8287 (pm20)
REVERT: A   71 THR cc_start: 0.8453 (t) cc_final: 0.7959 (t)
REVERT: A   75 ASP cc_start: 0.9329 (m-30) cc_final: 0.9040 (m-30)
REVERT: B  130 ASP cc_start: 0.8347 (t70) cc_final: 0.7542 (t0)
REVERT: B  197 MET cc_start: 0.8453 (ppp) cc_final: 0.8152 (ppp)
REVERT: B  268 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8858 (mm-30)
REVERT: B  331 LEU cc_start: 0.9224 (tp) cc_final: 0.9007 (tm)
REVERT: B  351 ASP cc_start: 0.9011 (p0) cc_final: 0.8724 (p0)
REVERT: B  372 MET cc_start: 0.8111 (tpp) cc_final: 0.7442 (tmm)
REVERT: B  418 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8959 (tm)
REVERT: C   46 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7123 (tm-30)
REVERT: C   82 MET cc_start: 0.8971 (mpt) cc_final: 0.8500 (mpm)
REVERT: C   85 LEU cc_start: 0.9149 (mm) cc_final: 0.8785 (mm)
REVERT: C  108 TRP cc_start: 0.8133 (m-10) cc_final: 0.7886 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 120
  average time/residue: 0.4039
  time to fit residues: 51.0209
Evaluate side-chains
  117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
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  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  407 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue   57 THR
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 19 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.069608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.057361 restraints weight = 14355.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 3.66
r_work: 0.2665 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5406  Z= 0.141
  Angle     :  0.722  10.956   7354  Z= 0.346
  Chirality :  0.041   0.146    880
  Planarity :  0.004   0.032    897
  Dihedral  :  3.955  19.481    732
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 25.44 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.03 (0.33), residues: 678
  helix:  2.40 (0.25), residues: 435
  sheet: -0.86 (0.96), residues: 35
  loop : -0.55 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 392 
 TYR   0.009   0.001   TYR C  94 
 PHE   0.016   0.001   PHE B 229 
 TRP   0.012   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5405)
  covalent geometry    : angle       0.72158 ( 7352)
  SS BOND              : bond        0.00445 (    1)
  SS BOND              : angle       1.60344 (    2)
  hydrogen bonds       : bond        0.04434 (  349)
  hydrogen bonds       : angle       3.83551 ( 1014)

*********************** 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
  123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8611 (pm20) cc_final: 0.8262 (pm20)
REVERT: A   71 THR cc_start: 0.8422 (t) cc_final: 0.7911 (t)
REVERT: A   75 ASP cc_start: 0.9332 (m-30) cc_final: 0.9065 (m-30)
REVERT: B  130 ASP cc_start: 0.8292 (t70) cc_final: 0.7422 (t0)
REVERT: B  268 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8835 (mm-30)
REVERT: B  294 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8050 (tp40)
REVERT: B  331 LEU cc_start: 0.9219 (tp) cc_final: 0.9016 (tm)
REVERT: B  351 ASP cc_start: 0.9041 (p0) cc_final: 0.8737 (p0)
REVERT: B  372 MET cc_start: 0.8163 (tpp) cc_final: 0.7422 (tmm)
REVERT: B  418 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8947 (tm)
REVERT: C   46 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7027 (tm-30)
REVERT: C   82 MET cc_start: 0.8956 (mpt) cc_final: 0.8487 (mpm)
REVERT: C   85 LEU cc_start: 0.9132 (mm) cc_final: 0.8772 (mm)
REVERT: C  108 TRP cc_start: 0.8115 (m-10) cc_final: 0.7308 (m-10)
  outliers start: 17
  outliers final: 10
  residues processed: 117
  average time/residue: 0.4254
  time to fit residues: 52.2214
Evaluate side-chains
  116 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  418 LEU
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 42 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0050
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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 = 0.3063 r_free = 0.3063 target = 0.070688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.058303 restraints weight = 14120.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 3.66
r_work: 0.2684 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5406  Z= 0.139
  Angle     :  0.750  12.094   7354  Z= 0.355
  Chirality :  0.041   0.141    880
  Planarity :  0.004   0.032    897
  Dihedral  :  3.898  18.870    732
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 25.26 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.01 (0.33), residues: 678
  helix:  2.37 (0.25), residues: 435
  sheet: -0.89 (0.96), residues: 35
  loop : -0.51 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 392 
 TYR   0.012   0.001   TYR B 129 
 PHE   0.015   0.001   PHE B 229 
 TRP   0.009   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5405)
  covalent geometry    : angle       0.74989 ( 7352)
  SS BOND              : bond        0.00441 (    1)
  SS BOND              : angle       1.43118 (    2)
  hydrogen bonds       : bond        0.04212 (  349)
  hydrogen bonds       : angle       3.80928 ( 1014)

*********************** 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: 20
    poor density    : 108
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8608 (pm20) cc_final: 0.8252 (pm20)
REVERT: A   71 THR cc_start: 0.8379 (t) cc_final: 0.7871 (t)
REVERT: A   75 ASP cc_start: 0.9330 (m-30) cc_final: 0.9060 (m-30)
REVERT: A  126 MET cc_start: 0.9269 (ttp) cc_final: 0.9053 (tmm)
REVERT: B  130 ASP cc_start: 0.8204 (t70) cc_final: 0.7251 (t0)
REVERT: B  268 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8830 (mm-30)
REVERT: B  294 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8067 (tp40)
REVERT: B  351 ASP cc_start: 0.9025 (p0) cc_final: 0.8729 (p0)
REVERT: B  372 MET cc_start: 0.8234 (tpp) cc_final: 0.7497 (tmm)
REVERT: B  418 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8995 (tm)
REVERT: C   46 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7090 (tm-30)
REVERT: C   82 MET cc_start: 0.8941 (mpt) cc_final: 0.8458 (mpm)
REVERT: C   85 LEU cc_start: 0.9103 (mm) cc_final: 0.8746 (mm)
REVERT: C  108 TRP cc_start: 0.8142 (m-10) cc_final: 0.7297 (m-10)
  outliers start: 20
  outliers final: 11
  residues processed: 119
  average time/residue: 0.4336
  time to fit residues: 54.3052
Evaluate side-chains
  117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  418 LEU
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 54 optimal weight:    0.1980
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
B 384 ASN
C  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.070601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.058398 restraints weight = 14114.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 3.64
r_work: 0.2688 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2307

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     :  0.790  16.298   7354  Z= 0.370
  Chirality :  0.041   0.143    880
  Planarity :  0.004   0.033    897
  Dihedral  :  3.919  18.743    732
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 26.67 %
    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 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:  1.90 (0.33), residues: 678
  helix:  2.28 (0.25), residues: 437
  sheet: -0.88 (0.96), residues: 35
  loop : -0.59 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 392 
 TYR   0.009   0.001   TYR A 103 
 PHE   0.019   0.001   PHE B 229 
 TRP   0.010   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5405)
  covalent geometry    : angle       0.78993 ( 7352)
  SS BOND              : bond        0.00482 (    1)
  SS BOND              : angle       1.58274 (    2)
  hydrogen bonds       : bond        0.04232 (  349)
  hydrogen bonds       : angle       3.83847 ( 1014)

*********************** 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
  127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8614 (pm20) cc_final: 0.8252 (pm20)
REVERT: A   66 ASP cc_start: 0.9099 (m-30) cc_final: 0.8820 (m-30)
REVERT: A   71 THR cc_start: 0.8383 (t) cc_final: 0.7884 (t)
REVERT: A   75 ASP cc_start: 0.9317 (m-30) cc_final: 0.9023 (m-30)
REVERT: B  120 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8651 (mt-10)
REVERT: B  130 ASP cc_start: 0.8262 (t70) cc_final: 0.7322 (t0)
REVERT: B  206 GLU cc_start: 0.8711 (pm20) cc_final: 0.8395 (pm20)
REVERT: B  268 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8856 (mm-30)
REVERT: B  294 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8207 (tp40)
REVERT: B  351 ASP cc_start: 0.9044 (p0) cc_final: 0.8750 (p0)
REVERT: B  372 MET cc_start: 0.8275 (tpp) cc_final: 0.7569 (tmm)
REVERT: B  418 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9034 (tm)
REVERT: C   46 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7116 (tm-30)
REVERT: C   82 MET cc_start: 0.8939 (mpt) cc_final: 0.8437 (mpm)
REVERT: C   85 LEU cc_start: 0.9073 (mm) cc_final: 0.8717 (mm)
REVERT: C  108 TRP cc_start: 0.8139 (m-10) cc_final: 0.7327 (m-10)
  outliers start: 16
  outliers final: 10
  residues processed: 119
  average time/residue: 0.4274
  time to fit residues: 53.5027
Evaluate side-chains
  117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 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  388 HIS
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  418 LEU
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 15 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0770
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0870
   overall best weight:    0.5320

-------------------------------------------------------------------------------
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 = 0.3074 r_free = 0.3074 target = 0.071430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.059115 restraints weight = 14216.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 3.66
r_work: 0.2709 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2446

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= 0.143
  Angle     :  0.766  12.377   7354  Z= 0.365
  Chirality :  0.041   0.155    880
  Planarity :  0.004   0.034    897
  Dihedral  :  3.890  18.316    732
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 26.84 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.87 (0.33), residues: 678
  helix:  2.26 (0.25), residues: 437
  sheet: -0.95 (0.97), residues: 35
  loop : -0.62 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 392 
 TYR   0.009   0.001   TYR A 103 
 PHE   0.019   0.001   PHE B 229 
 TRP   0.009   0.001   TRP C 108 
 HIS   0.004   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5405)
  covalent geometry    : angle       0.76544 ( 7352)
  SS BOND              : bond        0.00325 (    1)
  SS BOND              : angle       1.42466 (    2)
  hydrogen bonds       : bond        0.04055 (  349)
  hydrogen bonds       : angle       3.82966 ( 1014)

********************** 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
  123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.9075 (m-30) cc_final: 0.8788 (m-30)
REVERT: A   71 THR cc_start: 0.8358 (t) cc_final: 0.7854 (t)
REVERT: A   75 ASP cc_start: 0.9293 (m-30) cc_final: 0.8988 (m-30)
REVERT: B  129 TYR cc_start: 0.8967 (m-10) cc_final: 0.8597 (m-10)
REVERT: B  130 ASP cc_start: 0.8157 (t70) cc_final: 0.7282 (t0)
REVERT: B  206 GLU cc_start: 0.8705 (pm20) cc_final: 0.8398 (pm20)
REVERT: B  268 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8823 (mm-30)
REVERT: B  294 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8161 (tp40)
REVERT: B  351 ASP cc_start: 0.9049 (p0) cc_final: 0.8750 (p0)
REVERT: B  372 MET cc_start: 0.8350 (tpp) cc_final: 0.7648 (tmm)
REVERT: C   46 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7061 (tm-30)
REVERT: C   82 MET cc_start: 0.8916 (mpt) cc_final: 0.8400 (mpm)
REVERT: C  108 TRP cc_start: 0.8108 (m-10) cc_final: 0.7395 (m-10)
  outliers start: 16
  outliers final: 10
  residues processed: 117
  average time/residue: 0.4267
  time to fit residues: 52.3717
Evaluate side-chains
  115 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  331 LEU
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 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 34 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.3784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.069651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.057293 restraints weight = 14194.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 3.66
r_work: 0.2665 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5406  Z= 0.165
  Angle     :  0.808  14.907   7354  Z= 0.381
  Chirality :  0.042   0.193    880
  Planarity :  0.004   0.036    897
  Dihedral  :  3.964  19.005    732
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 27.19 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.94 (0.33), residues: 678
  helix:  2.34 (0.25), residues: 437
  sheet: -0.91 (0.95), residues: 35
  loop : -0.64 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 392 
 TYR   0.011   0.001   TYR B 425 
 PHE   0.025   0.001   PHE B 229 
 TRP   0.009   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5405)
  covalent geometry    : angle       0.80750 ( 7352)
  SS BOND              : bond        0.00559 (    1)
  SS BOND              : angle       1.62288 (    2)
  hydrogen bonds       : bond        0.04438 (  349)
  hydrogen bonds       : angle       3.89235 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1588.54 seconds
wall clock time: 27 minutes 51.39 seconds (1671.39 seconds total)