Starting phenix.real_space_refine
on Tue Feb  3 15:48:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i3u_52616/02_2026/9i3u_52616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i3u_52616/02_2026/9i3u_52616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i3u_52616/02_2026/9i3u_52616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i3u_52616/02_2026/9i3u_52616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i3u_52616/02_2026/9i3u_52616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i3u_52616/02_2026/9i3u_52616.cif"
  }
  resolution = 2.9
  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=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2853      2.51       5
     N     754      2.21       5
     O     820      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4445
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1081
          Classifications: {'peptide': 133}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126}
    Chain: "D"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1065
          Classifications: {'peptide': 131}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124}
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2299
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 274}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 0.93, per 1000 atoms: 0.21
  Number of scatterers: 4445
  At special positions: 0
  Unit cell: (64.881, 78.732, 97.686, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     820      8.00
     N     754      7.00
     C    2853      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 100.7 milliseconds
  

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1060

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 11 sheets defined
      23.6% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 57 through 69
    Processing helix  chain 'B' and resid 81 through 94
    Processing helix  chain 'B' and resid 94 through 102
      removed outlier: 3.836A  pdb=" N   GLU B 102 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 119
      removed outlier: 3.514A  pdb=" N   LEU B 118 " --> pdb=" O   ASP B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 169
      removed outlier: 3.506A  pdb=" N   LYS B 169 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 69
    Processing helix  chain 'D' and resid 81 through 93
    Processing helix  chain 'D' and resid 94 through 102
      removed outlier: 3.853A  pdb=" N   GLU D 102 " --> pdb=" O   GLN D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 119
      removed outlier: 3.617A  pdb=" N   LEU D 118 " --> pdb=" O   ASP D 115 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER D 119 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 115 through 119'
    Processing helix  chain 'D' and resid 156 through 169
      removed outlier: 3.525A  pdb=" N   LYS D 169 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 38
      No H-bonds generated for 'chain 'A' and resid 36 through 38'
    Processing helix  chain 'A' and resid 107 through 115
    Processing helix  chain 'A' and resid 249 through 260
    Processing sheet with id=AA1, first strand: chain 'B' and resid 105 through 109
      removed outlier: 6.132A  pdb=" N   MET B  73 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   LEU B 109 " --> pdb=" O   MET B  73 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ILE B  75 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 105 through 109
    Processing sheet with id=AA3, first strand: chain 'D' and resid 124 through 125
    Processing sheet with id=AA4, first strand: chain 'D' and resid 136 through 138
    Processing sheet with id=AA5, first strand: chain 'A' and resid 60 through 64
      removed outlier: 4.977A  pdb=" N   ALA A  52 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   THR A  63 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  50 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU A  40 " --> pdb=" O   TRP A 235 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   TRP A 235 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   VAL A 232 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 71
      removed outlier: 4.050A  pdb=" N   THR A 181 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 71
      removed outlier: 4.050A  pdb=" N   THR A 181 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 83
    Processing sheet with id=AA9, first strand: chain 'A' and resid 135 through 136
    Processing sheet with id=AB1, first strand: chain 'A' and resid 219 through 224
      removed outlier: 7.163A  pdb=" N   THR A 211 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   THR A 222 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LEU A 209 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   LEU A 208 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 296 through 305
      removed outlier: 3.536A  pdb=" N   GLY A 361 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)

    164 hydrogen bonds defined for protein.
    450 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: 0.62

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1408
        1.34 -     1.45: 667
        1.45 -     1.57: 2447
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 4554
  Sorted by residual:
  bond pdb=" CB  GLU B  80 "
       pdb=" CG  GLU B  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.06e+00
  bond pdb=" CB  GLU A 142 "
       pdb=" CG  GLU A 142 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.58e+00
  bond pdb=" CB  GLN A 237 "
       pdb=" CG  GLN A 237 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.44e+00
  bond pdb=" CB  GLU D  96 "
       pdb=" CG  GLU D  96 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" C   LEU A 317 "
       pdb=" O   LEU A 317 "
    ideal  model  delta    sigma   weight residual
    1.235  1.246 -0.011 1.03e-02 9.43e+03 1.08e+00
  ... (remaining 4549 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 6060
        1.68 -     3.36: 111
        3.36 -     5.04: 19
        5.04 -     6.73: 5
        6.73 -     8.41: 3
  Bond angle restraints: 6198
  Sorted by residual:
  angle pdb=" CA  GLN A 237 "
        pdb=" CB  GLN A 237 "
        pdb=" CG  GLN A 237 "
      ideal   model   delta    sigma   weight residual
     114.10  122.51   -8.41 2.00e+00 2.50e-01 1.77e+01
  angle pdb=" N   GLN A 237 "
        pdb=" CA  GLN A 237 "
        pdb=" CB  GLN A 237 "
      ideal   model   delta    sigma   weight residual
     110.49  116.60   -6.11 1.69e+00 3.50e-01 1.31e+01
  angle pdb=" CA  GLU B  80 "
        pdb=" CB  GLU B  80 "
        pdb=" CG  GLU B  80 "
      ideal   model   delta    sigma   weight residual
     114.10  120.98   -6.88 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" CB  GLU B  80 "
        pdb=" CG  GLU B  80 "
        pdb=" CD  GLU B  80 "
      ideal   model   delta    sigma   weight residual
     112.60  118.27   -5.67 1.70e+00 3.46e-01 1.11e+01
  angle pdb=" CA  GLU A 142 "
        pdb=" CB  GLU A 142 "
        pdb=" CG  GLU A 142 "
      ideal   model   delta    sigma   weight residual
     114.10  119.80   -5.70 2.00e+00 2.50e-01 8.13e+00
  ... (remaining 6193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 2357
       17.01 -    34.01: 237
       34.01 -    51.02: 99
       51.02 -    68.03: 21
       68.03 -    85.03: 17
  Dihedral angle restraints: 2731
    sinusoidal: 1091
      harmonic: 1640
  Sorted by residual:
  dihedral pdb=" CA  HIS A 236 "
           pdb=" C   HIS A 236 "
           pdb=" N   GLN A 237 "
           pdb=" CA  GLN A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  THR A 316 "
           pdb=" C   THR A 316 "
           pdb=" N   LEU A 317 "
           pdb=" CA  LEU A 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.21  -19.79     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  LEU A 315 "
           pdb=" C   LEU A 315 "
           pdb=" N   THR A 316 "
           pdb=" CA  THR A 316 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.52   17.48     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 2728 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 521
       0.038 -    0.075: 131
       0.075 -    0.113: 52
       0.113 -    0.150: 7
       0.150 -    0.188: 1
  Chirality restraints: 712
  Sorted by residual:
  chirality pdb=" CA  GLN A 237 "
            pdb=" N   GLN A 237 "
            pdb=" C   GLN A 237 "
            pdb=" CB  GLN A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CA  ILE A  92 "
            pdb=" N   ILE A  92 "
            pdb=" C   ILE A  92 "
            pdb=" CB  ILE A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  VAL D 105 "
            pdb=" N   VAL D 105 "
            pdb=" C   VAL D 105 "
            pdb=" CB  VAL D 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 709 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 188 "    0.042 5.00e-02 4.00e+02   6.42e-02 6.59e+00
        pdb=" N   PRO A 189 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  36 "    0.035 5.00e-02 4.00e+02   5.41e-02 4.68e+00
        pdb=" N   PRO A  37 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A  37 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  37 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 132 "   -0.035 5.00e-02 4.00e+02   5.38e-02 4.64e+00
        pdb=" N   PRO B 133 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 133 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 133 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 2154
        2.99 -     3.47: 4241
        3.47 -     3.95: 7296
        3.95 -     4.42: 8346
        4.42 -     4.90: 13763
  Nonbonded interactions: 35800
  Sorted by model distance:
  nonbonded pdb=" N   GLU D  96 "
            pdb=" OE1 GLU D  96 "
     model   vdw
     2.517 3.120
  nonbonded pdb=" O   GLU B  80 "
            pdb=" OE1 GLU B  80 "
     model   vdw
     2.555 3.040
  nonbonded pdb=" O   HIS A 236 "
            pdb=" OE1 GLN A 237 "
     model   vdw
     2.605 3.040
  nonbonded pdb=" O   SER D 134 "
            pdb=" OG  SER D 134 "
     model   vdw
     2.607 3.040
  nonbonded pdb=" O   LEU A 353 "
            pdb=" N   SER A 355 "
     model   vdw
     2.609 3.120
  ... (remaining 35795 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 41 through 171)
  selection = chain 'D'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.880
  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:                     5.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:6.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
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   0.043   4554  Z= 0.143
  Angle     :  0.618   8.408   6198  Z= 0.331
  Chirality :  0.040   0.188    712
  Planarity :  0.006   0.064    776
  Dihedral  : 18.171  85.034   1671
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 26.84 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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: -0.07 (0.35), residues: 547
  helix:  2.13 (0.49), residues: 114
  sheet: -0.11 (0.40), residues: 146
  loop : -0.91 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  46 
 TYR   0.011   0.001   TYR D 111 
 PHE   0.011   0.002   PHE D  91 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.006   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4554)
  covalent geometry    : angle       0.61770 ( 6198)
  hydrogen bonds       : bond        0.14433 (  159)
  hydrogen bonds       : angle       8.78582 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: D  102 GLU cc_start: 0.8247 (mp0) cc_final: 0.7902 (mp0)
REVERT: A  335 GLU cc_start: 0.8670 (mp0) cc_final: 0.8412 (mp0)
REVERT: A  337 GLU cc_start: 0.7769 (pt0) cc_final: 0.7530 (pt0)
  outliers start: 7
  outliers final: 1
  residues processed: 82
  average time/residue: 0.5138
  time to fit residues: 43.4445
Evaluate side-chains
  61 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0050
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0050
   chunk 53 optimal weight:    0.0050
   overall best weight:    0.1822

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

Flipped N/Q/H residues before XYZ refinement:
B 123 GLN
D  85 GLN
A 163 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.064398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.051763 restraints weight = 12446.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 3.01
r_work: 0.2712 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4554  Z= 0.098
  Angle     :  0.544  10.104   6198  Z= 0.267
  Chirality :  0.039   0.139    712
  Planarity :  0.005   0.068    776
  Dihedral  :  4.342  38.904    607
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.16 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.51 (0.36), residues: 547
  helix:  2.66 (0.50), residues: 114
  sheet:  0.40 (0.41), residues: 144
  loop : -0.66 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 144 
 TYR   0.012   0.001   TYR A 125 
 PHE   0.010   0.001   PHE A  81 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4554)
  covalent geometry    : angle       0.54437 ( 6198)
  hydrogen bonds       : bond        0.02995 (  159)
  hydrogen bonds       : angle       5.65504 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   93 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7466 (mp0)
REVERT: D  102 GLU cc_start: 0.8473 (mp0) cc_final: 0.7859 (mp0)
REVERT: D  153 GLU cc_start: 0.8892 (mt-10) cc_final: 0.7961 (mt-10)
REVERT: A  335 GLU cc_start: 0.8867 (mp0) cc_final: 0.8555 (mp0)
  outliers start: 16
  outliers final: 3
  residues processed: 75
  average time/residue: 0.4514
  time to fit residues: 35.0883
Evaluate side-chains
  62 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  262 HIS
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.060898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.048194 restraints weight = 12375.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 3.05
r_work: 0.2615 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4554  Z= 0.196
  Angle     :  0.597  10.278   6198  Z= 0.288
  Chirality :  0.042   0.206    712
  Planarity :  0.005   0.069    776
  Dihedral  :  4.545  40.603    607
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.98 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.51 (0.35), residues: 547
  helix:  2.53 (0.49), residues: 115
  sheet:  0.56 (0.41), residues: 144
  loop : -0.70 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 183 
 TYR   0.012   0.001   TYR B 150 
 PHE   0.011   0.002   PHE D  91 
 TRP   0.015   0.001   TRP B  48 
 HIS   0.008   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 4554)
  covalent geometry    : angle       0.59657 ( 6198)
  hydrogen bonds       : bond        0.03644 (  159)
  hydrogen bonds       : angle       4.91447 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: D  102 GLU cc_start: 0.8497 (mp0) cc_final: 0.7879 (mp0)
REVERT: A  241 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (mmm-85)
REVERT: A  335 GLU cc_start: 0.8932 (mp0) cc_final: 0.8584 (mp0)
REVERT: A  337 GLU cc_start: 0.7971 (pt0) cc_final: 0.7619 (pt0)
  outliers start: 14
  outliers final: 3
  residues processed: 67
  average time/residue: 0.5224
  time to fit residues: 36.1690
Evaluate side-chains
  57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  241 ARG
Chi-restraints excluded: chain A residue  262 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 123 GLN
A 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.060740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.048284 restraints weight = 12438.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 2.98
r_work: 0.2627 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4554  Z= 0.181
  Angle     :  0.568  11.143   6198  Z= 0.275
  Chirality :  0.041   0.240    712
  Planarity :  0.005   0.070    776
  Dihedral  :  4.521  41.735    607
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.98 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.59 (0.36), residues: 547
  helix:  2.52 (0.50), residues: 115
  sheet:  0.78 (0.41), residues: 144
  loop : -0.72 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 144 
 TYR   0.009   0.001   TYR B 150 
 PHE   0.012   0.001   PHE D  91 
 TRP   0.009   0.001   TRP B  48 
 HIS   0.004   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 4554)
  covalent geometry    : angle       0.56822 ( 6198)
  hydrogen bonds       : bond        0.03222 (  159)
  hydrogen bonds       : angle       4.70075 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8352 (tp30)
REVERT: D  102 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7943 (mp0)
REVERT: A  190 MET cc_start: 0.8479 (tpt) cc_final: 0.7911 (tpt)
REVERT: A  241 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8435 (mmm-85)
REVERT: A  335 GLU cc_start: 0.8945 (mp0) cc_final: 0.8595 (mp0)
  outliers start: 13
  outliers final: 3
  residues processed: 65
  average time/residue: 0.6124
  time to fit residues: 41.1061
Evaluate side-chains
  59 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  241 ARG
Chi-restraints excluded: chain A residue  262 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0070
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0370
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0970
   overall best weight:    0.3474

-------------------------------------------------------------------------------
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 = 0.3096 r_free = 0.3096 target = 0.062055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.049459 restraints weight = 12396.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 3.03
r_work: 0.2655 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4554  Z= 0.103
  Angle     :  0.531  11.044   6198  Z= 0.258
  Chirality :  0.040   0.219    712
  Planarity :  0.005   0.076    776
  Dihedral  :  4.307  40.605    607
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 26.23 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.72 (0.36), residues: 547
  helix:  2.70 (0.50), residues: 115
  sheet:  0.83 (0.42), residues: 142
  loop : -0.65 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 144 
 TYR   0.009   0.001   TYR A 197 
 PHE   0.010   0.001   PHE D  91 
 TRP   0.005   0.001   TRP B  48 
 HIS   0.004   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 4554)
  covalent geometry    : angle       0.53086 ( 6198)
  hydrogen bonds       : bond        0.02691 (  159)
  hydrogen bonds       : angle       4.44269 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8259 (tp30)
REVERT: D  102 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7907 (mp0)
REVERT: A  241 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8458 (mmm-85)
REVERT: A  335 GLU cc_start: 0.8939 (mp0) cc_final: 0.8581 (mp0)
REVERT: A  337 GLU cc_start: 0.7853 (pt0) cc_final: 0.7636 (pt0)
  outliers start: 7
  outliers final: 3
  residues processed: 62
  average time/residue: 0.6500
  time to fit residues: 41.4500
Evaluate side-chains
  58 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  241 ARG
Chi-restraints excluded: chain A residue  262 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0070
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.060188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.047654 restraints weight = 12724.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 3.05
r_work: 0.2607 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4554  Z= 0.205
  Angle     :  0.577  11.231   6198  Z= 0.280
  Chirality :  0.042   0.267    712
  Planarity :  0.005   0.073    776
  Dihedral  :  4.485  42.210    607
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 25.41 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.59 (0.36), residues: 547
  helix:  2.56 (0.50), residues: 115
  sheet:  0.79 (0.41), residues: 145
  loop : -0.75 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 250 
 TYR   0.011   0.001   TYR A 197 
 PHE   0.013   0.002   PHE D  91 
 TRP   0.012   0.001   TRP B  48 
 HIS   0.004   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 4554)
  covalent geometry    : angle       0.57737 ( 6198)
  hydrogen bonds       : bond        0.03365 (  159)
  hydrogen bonds       : angle       4.55050 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8296 (tp30)
REVERT: D  102 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7917 (mp0)
REVERT: A  190 MET cc_start: 0.8483 (tpt) cc_final: 0.8079 (tpt)
REVERT: A  241 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8552 (mmm-85)
REVERT: A  335 GLU cc_start: 0.8910 (mp0) cc_final: 0.8520 (mp0)
REVERT: A  364 GLU cc_start: 0.8368 (mp0) cc_final: 0.8139 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 61
  average time/residue: 0.4588
  time to fit residues: 28.8734
Evaluate side-chains
  59 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain D residue  156 ASP
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  241 ARG
Chi-restraints excluded: chain A residue  262 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3064 r_free = 0.3064 target = 0.060598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.048250 restraints weight = 12575.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 3.01
r_work: 0.2618 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4554  Z= 0.163
  Angle     :  0.560  11.398   6198  Z= 0.272
  Chirality :  0.041   0.231    712
  Planarity :  0.005   0.073    776
  Dihedral  :  4.426  41.140    607
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 25.82 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.58 (0.36), residues: 547
  helix:  2.62 (0.50), residues: 115
  sheet:  0.77 (0.41), residues: 145
  loop : -0.77 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 250 
 TYR   0.009   0.001   TYR A 197 
 PHE   0.012   0.001   PHE D  91 
 TRP   0.008   0.001   TRP B  48 
 HIS   0.004   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 4554)
  covalent geometry    : angle       0.56036 ( 6198)
  hydrogen bonds       : bond        0.03063 (  159)
  hydrogen bonds       : angle       4.47813 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8307 (tp30)
REVERT: D  102 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7907 (mp0)
REVERT: A  335 GLU cc_start: 0.8910 (mp0) cc_final: 0.8526 (mp0)
REVERT: A  337 GLU cc_start: 0.7898 (pt0) cc_final: 0.7556 (pt0)
REVERT: A  364 GLU cc_start: 0.8345 (mp0) cc_final: 0.8123 (mp0)
  outliers start: 10
  outliers final: 6
  residues processed: 62
  average time/residue: 0.6731
  time to fit residues: 42.9983
Evaluate side-chains
  58 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain D residue  156 ASP
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  262 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.0970
   chunk 50 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0050
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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 = 0.3094 r_free = 0.3094 target = 0.061898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.049218 restraints weight = 12538.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 3.05
r_work: 0.2652 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4554  Z= 0.104
  Angle     :  0.540  11.600   6198  Z= 0.262
  Chirality :  0.040   0.219    712
  Planarity :  0.005   0.072    776
  Dihedral  :  4.212  39.021    607
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 26.64 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.71 (0.36), residues: 547
  helix:  2.79 (0.51), residues: 115
  sheet:  0.78 (0.41), residues: 142
  loop : -0.66 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 250 
 TYR   0.009   0.001   TYR A 197 
 PHE   0.011   0.001   PHE D  91 
 TRP   0.004   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4554)
  covalent geometry    : angle       0.54032 ( 6198)
  hydrogen bonds       : bond        0.02629 (  159)
  hydrogen bonds       : angle       4.29744 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8236 (tp30)
REVERT: D  102 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7932 (mp0)
REVERT: A  335 GLU cc_start: 0.8894 (mp0) cc_final: 0.8517 (mp0)
REVERT: A  337 GLU cc_start: 0.7816 (pt0) cc_final: 0.7487 (pt0)
  outliers start: 5
  outliers final: 2
  residues processed: 56
  average time/residue: 0.7043
  time to fit residues: 40.7796
Evaluate side-chains
  54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 37 optimal weight:    0.4980
   chunk 24 optimal weight:    0.1980
   chunk 7 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3090 r_free = 0.3090 target = 0.061664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.049155 restraints weight = 12473.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 3.02
r_work: 0.2645 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4554  Z= 0.126
  Angle     :  0.558  11.554   6198  Z= 0.271
  Chirality :  0.040   0.214    712
  Planarity :  0.005   0.071    776
  Dihedral  :  3.879  17.787    605
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 26.64 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.72 (0.36), residues: 547
  helix:  2.79 (0.51), residues: 115
  sheet:  0.81 (0.41), residues: 142
  loop : -0.67 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 250 
 TYR   0.009   0.001   TYR A 197 
 PHE   0.013   0.001   PHE D  91 
 TRP   0.007   0.001   TRP B  48 
 HIS   0.002   0.001   HIS D  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4554)
  covalent geometry    : angle       0.55794 ( 6198)
  hydrogen bonds       : bond        0.02759 (  159)
  hydrogen bonds       : angle       4.26008 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8259 (tp30)
REVERT: D  102 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7892 (mp0)
REVERT: A  335 GLU cc_start: 0.8871 (mp0) cc_final: 0.8489 (mp0)
REVERT: A  337 GLU cc_start: 0.7857 (pt0) cc_final: 0.7561 (pt0)
  outliers start: 5
  outliers final: 3
  residues processed: 55
  average time/residue: 0.7080
  time to fit residues: 40.2728
Evaluate side-chains
  55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  262 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0770
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3084 r_free = 0.3084 target = 0.061520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.048835 restraints weight = 12625.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 3.05
r_work: 0.2640 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4554  Z= 0.133
  Angle     :  0.555  11.509   6198  Z= 0.268
  Chirality :  0.040   0.221    712
  Planarity :  0.005   0.072    776
  Dihedral  :  3.909  17.534    605
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 27.05 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.74 (0.36), residues: 547
  helix:  2.79 (0.51), residues: 115
  sheet:  0.81 (0.41), residues: 142
  loop : -0.64 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 250 
 TYR   0.008   0.001   TYR A 197 
 PHE   0.012   0.001   PHE D  91 
 TRP   0.007   0.001   TRP B  48 
 HIS   0.004   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4554)
  covalent geometry    : angle       0.55461 ( 6198)
  hydrogen bonds       : bond        0.02815 (  159)
  hydrogen bonds       : angle       4.28223 (  450)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8243 (tp30)
REVERT: D  102 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7902 (mp0)
REVERT: A  335 GLU cc_start: 0.8877 (mp0) cc_final: 0.8496 (mp0)
REVERT: A  337 GLU cc_start: 0.7868 (pt0) cc_final: 0.7567 (pt0)
REVERT: A  364 GLU cc_start: 0.8346 (mp0) cc_final: 0.8127 (mp0)
  outliers start: 4
  outliers final: 3
  residues processed: 54
  average time/residue: 0.7429
  time to fit residues: 41.4165
Evaluate side-chains
  54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  262 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3093 r_free = 0.3093 target = 0.061898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.049246 restraints weight = 12496.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 3.04
r_work: 0.2654 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4554  Z= 0.114
  Angle     :  0.547  11.453   6198  Z= 0.265
  Chirality :  0.040   0.217    712
  Planarity :  0.005   0.072    776
  Dihedral  :  3.892  17.271    605
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 27.05 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    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:  0.76 (0.36), residues: 547
  helix:  2.83 (0.51), residues: 115
  sheet:  0.78 (0.41), residues: 144
  loop : -0.63 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 250 
 TYR   0.010   0.001   TYR D 145 
 PHE   0.011   0.001   PHE D  91 
 TRP   0.006   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4554)
  covalent geometry    : angle       0.54727 ( 6198)
  hydrogen bonds       : bond        0.02685 (  159)
  hydrogen bonds       : angle       4.23622 (  450)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1439.87 seconds
wall clock time: 25 minutes 19.41 seconds (1519.41 seconds total)