Starting phenix.real_space_refine
on Fri May  9 13:43:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j46_35971/05_2025/8j46_35971_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j46_35971/05_2025/8j46_35971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j46_35971/05_2025/8j46_35971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j46_35971/05_2025/8j46_35971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j46_35971/05_2025/8j46_35971_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j46_35971/05_2025/8j46_35971_neut.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.010
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       4      5.16       5
     C    1381      2.51       5
     N     383      2.21       5
     O     390      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2158
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2158
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 204}
          Link IDs: {'PTRANS': 14, 'TRANS': 347}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 733
          Unresolved non-hydrogen angles: 931
          Unresolved non-hydrogen dihedrals: 601
          Unresolved non-hydrogen chiralities: 88
          Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 10, 'GLU:plan': 12, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 340
  Time building chain proxies: 2.82, per 1000 atoms: 1.31
  Number of scatterers: 2158
  At special positions: 0
  Unit cell: (60.208, 80.56, 109.392, 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       4     16.00
     O     390      8.00
     N     383      7.00
     C    1381      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 181 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 444.7 milliseconds
  

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  696

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 1 sheets defined
      87.3% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 52
      removed outlier: 4.342A  pdb=" N   PHE A  33 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 77
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 3.637A  pdb=" N   MET A  83 " --> pdb=" O   THR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 130
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 139 through 159
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 4.118A  pdb=" N   PHE A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 188
      removed outlier: 3.673A  pdb=" N   LYS A 188 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 209
      removed outlier: 3.820A  pdb=" N   TYR A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 1019
      removed outlier: 3.634A  pdb=" N   ILE A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA A 996 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ARG A 997 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ARG A 998 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A1003 " --> pdb=" O   GLN A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1044
      removed outlier: 3.567A  pdb=" N   LYS A1032 " --> pdb=" O   ASP A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1062 through 1081
      removed outlier: 3.632A  pdb=" N   ASP A1066 " --> pdb=" O   ARG A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 242
      removed outlier: 3.855A  pdb=" N   ALA A1087 " --> pdb=" O   LYS A1083 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   THR A1096 " --> pdb=" O   GLU A1092 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   THR A1097 " --> pdb=" O   GLN A1093 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN A1103 " --> pdb=" O   ASN A1099 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LYS A1104 " --> pdb=" O   ALA A1100 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG A1110 " --> pdb=" O   LEU A1106 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   SER A1111 " --> pdb=" O   GLU A1107 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A1110 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS A 238 " --> pdb=" O   SER A1111 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ALA A 239 " --> pdb=" O   THR A1112 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU A 240 " --> pdb=" O   LEU A1113 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 264
      removed outlier: 3.641A  pdb=" N   ILE A 247 " --> pdb=" O   CYS A 243 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   CYS A 248 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 271 through 294
      removed outlier: 3.586A  pdb=" N   HIS A 275 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
      Proline residue:  A 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95
      removed outlier: 8.868A  pdb=" N   ILE A 176 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LEU A  15 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)

    216 hydrogen bonds defined for protein.
    648 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: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 643
        1.33 -     1.45: 278
        1.45 -     1.57: 1269
        1.57 -     1.69: 0
        1.69 -     1.80: 4
  Bond restraints: 2194
  Sorted by residual:
  bond pdb=" N   PRO A  11 "
       pdb=" CD  PRO A  11 "
    ideal  model  delta    sigma   weight residual
    1.473  1.528 -0.055 1.40e-02 5.10e+03 1.55e+01
  bond pdb=" C   MET A 112 "
       pdb=" O   MET A 112 "
    ideal  model  delta    sigma   weight residual
    1.237  1.218  0.019 1.19e-02 7.06e+03 2.48e+00
  bond pdb=" N   HIS A1063 "
       pdb=" CA  HIS A1063 "
    ideal  model  delta    sigma   weight residual
    1.459  1.441  0.018 1.21e-02 6.83e+03 2.18e+00
  bond pdb=" C   MET A 112 "
       pdb=" N   GLU A 113 "
    ideal  model  delta    sigma   weight residual
    1.335  1.316  0.019 1.31e-02 5.83e+03 2.13e+00
  bond pdb=" C   LEU A 156 "
       pdb=" O   LEU A 156 "
    ideal  model  delta    sigma   weight residual
    1.237  1.220  0.017 1.17e-02 7.31e+03 2.01e+00
  ... (remaining 2189 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 2902
        1.51 -     3.02: 102
        3.02 -     4.53: 19
        4.53 -     6.04: 14
        6.04 -     7.55: 3
  Bond angle restraints: 3040
  Sorted by residual:
  angle pdb=" N   ALA A 226 "
        pdb=" CA  ALA A 226 "
        pdb=" C   ALA A 226 "
      ideal   model   delta    sigma   weight residual
     111.36  117.35   -5.99 1.09e+00 8.42e-01 3.02e+01
  angle pdb=" N   THR A1112 "
        pdb=" CA  THR A1112 "
        pdb=" C   THR A1112 "
      ideal   model   delta    sigma   weight residual
     111.36  117.21   -5.85 1.09e+00 8.42e-01 2.88e+01
  angle pdb=" N   LEU A 237 "
        pdb=" CA  LEU A 237 "
        pdb=" C   LEU A 237 "
      ideal   model   delta    sigma   weight residual
     111.28  116.26   -4.98 1.09e+00 8.42e-01 2.09e+01
  angle pdb=" N   LYS A1015 "
        pdb=" CA  LYS A1015 "
        pdb=" C   LYS A1015 "
      ideal   model   delta    sigma   weight residual
     111.28  106.42    4.86 1.09e+00 8.42e-01 1.99e+01
  angle pdb=" N   ASN A1022 "
        pdb=" CA  ASN A1022 "
        pdb=" C   ASN A1022 "
      ideal   model   delta    sigma   weight residual
     109.24  115.74   -6.50 1.51e+00 4.39e-01 1.86e+01
  ... (remaining 3035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.19: 1176
        9.19 -    18.37: 51
       18.37 -    27.56: 25
       27.56 -    36.74: 19
       36.74 -    45.93: 4
  Dihedral angle restraints: 1275
    sinusoidal: 213
      harmonic: 1062
  Sorted by residual:
  dihedral pdb=" CB  CYS A  99 "
           pdb=" SG  CYS A  99 "
           pdb=" SG  CYS A 181 "
           pdb=" CB  CYS A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -118.25   32.25     1      1.00e+01 1.00e-02 1.48e+01
  dihedral pdb=" CA  LEU A 164 "
           pdb=" CB  LEU A 164 "
           pdb=" CG  LEU A 164 "
           pdb=" CD1 LEU A 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.88   42.12     3      1.50e+01 4.44e-03 7.55e+00
  dihedral pdb=" N   LEU A1038 "
           pdb=" CA  LEU A1038 "
           pdb=" CB  LEU A1038 "
           pdb=" CG  LEU A1038 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.23   41.23     3      1.50e+01 4.44e-03 7.37e+00
  ... (remaining 1272 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 326
       0.061 -    0.122: 56
       0.122 -    0.183: 9
       0.183 -    0.244: 2
       0.244 -    0.305: 1
  Chirality restraints: 394
  Sorted by residual:
  chirality pdb=" CA  TYR A1101 "
            pdb=" N   TYR A1101 "
            pdb=" C   TYR A1101 "
            pdb=" CB  TYR A1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" CA  ASP A1021 "
            pdb=" N   ASP A1021 "
            pdb=" C   ASP A1021 "
            pdb=" CB  ASP A1021 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ALA A 226 "
            pdb=" N   ALA A 226 "
            pdb=" C   ALA A 226 "
            pdb=" CB  ALA A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.20 2.00e-01 2.50e+01 9.58e-01
  ... (remaining 391 not shown)

  Planarity restraints: 406
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 225 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   ARG A 225 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ARG A 225 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ALA A 226 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 159 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO A 160 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 160 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 160 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 286 "    0.037 5.00e-02 4.00e+02   5.59e-02 5.00e+00
        pdb=" N   PRO A 287 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "    0.032 5.00e-02 4.00e+02
  ... (remaining 403 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 1006
        2.95 -     3.44: 2404
        3.44 -     3.93: 3253
        3.93 -     4.41: 3225
        4.41 -     4.90: 5483
  Nonbonded interactions: 15371
  Sorted by model distance:
  nonbonded pdb=" O   THR A 135 "
            pdb=" O   LEU A 138 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" ND2 ASN A  44 "
            pdb=" OD2 ASP A  72 "
     model   vdw
     2.506 3.120
  nonbonded pdb=" O   ASP A1005 "
            pdb=" OD1 ASP A1005 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" O   ASN A1013 "
            pdb=" OD1 ASN A1013 "
     model   vdw
     2.563 3.040
  nonbonded pdb=" O   VAL A1016 "
            pdb=" O   LYS A1019 "
     model   vdw
     2.577 3.040
  ... (remaining 15366 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.830
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.530
  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:             0.000
  Load rotamer database and sin/cos tables:2.970
  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: 0.7369
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      :  0.004   0.055   2195  Z= 0.241
  Angle     :  0.772   7.551   3042  Z= 0.525
  Chirality :  0.052   0.305    394
  Planarity :  0.006   0.059    406
  Dihedral  :  9.516  45.928    576
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 0.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.35 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.46), residues: 350
  helix:  2.46 (0.31), residues: 282
  sheet:  None (None), residues: 0
  loop : -1.28 (0.72), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 183 
 PHE   0.004   0.001   PHE A 161 
 TYR   0.008   0.001   TYR A 134 
 ARG   0.001   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17270 (  216)
  hydrogen bonds       : angle       6.17487 (  648)
  SS BOND              : bond        0.00173 (    1)
  SS BOND              : angle       0.18290 (    2)
  covalent geometry    : bond        0.00375 ( 2194)
  covalent geometry    : angle       0.77246 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.242 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0725
  time to fit residues: 5.3442
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1006 ASN
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.074085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.063967 restraints weight = 14419.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.065065 restraints weight = 9791.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.065764 restraints weight = 7440.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   2195  Z= 0.284
  Angle     :  0.711   7.400   3042  Z= 0.398
  Chirality :  0.045   0.132    394
  Planarity :  0.005   0.049    406
  Dihedral  :  3.872  15.560    367
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.08 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.45), residues: 350
  helix:  1.75 (0.30), residues: 298
  sheet:  None (None), residues: 0
  loop : -2.77 (0.73), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.013   0.004   HIS A 178 
 PHE   0.026   0.003   PHE A  87 
 TYR   0.014   0.002   TYR A  62 
 ARG   0.004   0.002   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06328 (  216)
  hydrogen bonds       : angle       4.93476 (  648)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       2.10775 (    2)
  covalent geometry    : bond        0.00552 ( 2194)
  covalent geometry    : angle       0.70869 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8970 (t80) cc_final: 0.8660 (t80)
  outliers start: 4
  outliers final: 1
  residues processed: 34
  average time/residue: 0.0737
  time to fit residues: 3.4846
Evaluate side-chains
  30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.076071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.066162 restraints weight = 14028.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.067207 restraints weight = 9472.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.068009 restraints weight = 7232.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2195  Z= 0.130
  Angle     :  0.541   7.279   3042  Z= 0.278
  Chirality :  0.040   0.126    394
  Planarity :  0.004   0.048    406
  Dihedral  :  3.269  11.204    367
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 23.08 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.46), residues: 350
  helix:  2.60 (0.30), residues: 298
  sheet:  None (None), residues: 0
  loop : -2.67 (0.72), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.006   0.002   HIS A 178 
 PHE   0.009   0.002   PHE A  87 
 TYR   0.007   0.001   TYR A 125 
 ARG   0.001   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04662 (  216)
  hydrogen bonds       : angle       4.00958 (  648)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       1.48309 (    2)
  covalent geometry    : bond        0.00259 ( 2194)
  covalent geometry    : angle       0.54016 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.240 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 36
  average time/residue: 0.0680
  time to fit residues: 3.4292
Evaluate side-chains
  33 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   99 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 1 optimal weight:   20.0000
   chunk 0 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.075551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.065443 restraints weight = 13889.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066555 restraints weight = 9378.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.067395 restraints weight = 7045.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2195  Z= 0.150
  Angle     :  0.534   5.271   3042  Z= 0.282
  Chirality :  0.040   0.141    394
  Planarity :  0.004   0.041    406
  Dihedral  :  3.316  12.642    367
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 23.08 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.47), residues: 350
  helix:  2.65 (0.31), residues: 306
  sheet:  None (None), residues: 0
  loop : -2.97 (0.79), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.032   0.002   PHE A  87 
 TYR   0.014   0.002   TYR A  37 
 ARG   0.001   0.001   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04639 (  216)
  hydrogen bonds       : angle       3.96396 (  648)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       1.41599 (    2)
  covalent geometry    : bond        0.00307 ( 2194)
  covalent geometry    : angle       0.53337 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   80 ILE cc_start: 0.9421 (mm) cc_final: 0.9163 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0686
  time to fit residues: 3.6277
Evaluate side-chains
  35 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0270
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A1006 ASN
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.077679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.067692 restraints weight = 14188.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.068906 restraints weight = 9088.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.069783 restraints weight = 6674.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   2195  Z= 0.112
  Angle     :  0.495   6.529   3042  Z= 0.256
  Chirality :  0.039   0.145    394
  Planarity :  0.004   0.040    406
  Dihedral  :  3.084  11.711    367
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 25.96 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.41 (0.48), residues: 350
  helix:  2.94 (0.31), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.91 (0.75), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 246 
 PHE   0.010   0.001   PHE A  87 
 TYR   0.017   0.001   TYR A  37 
 ARG   0.000   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  216)
  hydrogen bonds       : angle       3.54975 (  648)
  SS BOND              : bond        0.00350 (    1)
  SS BOND              : angle       1.79305 (    2)
  covalent geometry    : bond        0.00218 ( 2194)
  covalent geometry    : angle       0.49311 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8769 (t80) cc_final: 0.8123 (t80)
REVERT: A   80 ILE cc_start: 0.9389 (mm) cc_final: 0.9006 (mt)
  outliers start: 6
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0667
  time to fit residues: 3.6914
Evaluate side-chains
  38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.077691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.067605 restraints weight = 13952.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.068796 restraints weight = 9099.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.069692 restraints weight = 6712.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2195  Z= 0.116
  Angle     :  0.523   5.802   3042  Z= 0.273
  Chirality :  0.039   0.151    394
  Planarity :  0.004   0.040    406
  Dihedral  :  3.137  14.457    367
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.96 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.46 (0.47), residues: 350
  helix:  2.94 (0.31), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.48 (0.80), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.016   0.001   PHE A  87 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.000   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  216)
  hydrogen bonds       : angle       3.64716 (  648)
  SS BOND              : bond        0.01009 (    1)
  SS BOND              : angle       5.49406 (    2)
  covalent geometry    : bond        0.00234 ( 2194)
  covalent geometry    : angle       0.50432 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8828 (t80) cc_final: 0.8328 (t80)
REVERT: A   80 ILE cc_start: 0.9380 (mm) cc_final: 0.9128 (tp)
  outliers start: 4
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0726
  time to fit residues: 3.9773
Evaluate side-chains
  36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0570
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0040
   chunk 18 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    0.9712

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.077626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.067628 restraints weight = 13892.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.068841 restraints weight = 8935.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.069701 restraints weight = 6588.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   2195  Z= 0.109
  Angle     :  0.487   5.028   3042  Z= 0.254
  Chirality :  0.039   0.162    394
  Planarity :  0.004   0.039    406
  Dihedral  :  3.007  10.506    367
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 26.92 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.48 (0.47), residues: 350
  helix:  2.97 (0.30), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.60 (0.80), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.034   0.002   PHE A  87 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.000   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  216)
  hydrogen bonds       : angle       3.43480 (  648)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       1.01403 (    2)
  covalent geometry    : bond        0.00228 ( 2194)
  covalent geometry    : angle       0.48631 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8825 (t80) cc_final: 0.8505 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0698
  time to fit residues: 3.8587
Evaluate side-chains
  37 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0970
   chunk 33 optimal weight:    0.0000
   chunk 1 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0770
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.4342

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.076291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066012 restraints weight = 14198.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.067103 restraints weight = 9535.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.067930 restraints weight = 7202.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2195  Z= 0.123
  Angle     :  0.495   4.923   3042  Z= 0.259
  Chirality :  0.040   0.177    394
  Planarity :  0.004   0.039    406
  Dihedral  :  3.071  10.212    367
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 28.85 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.48 (0.47), residues: 350
  helix:  2.98 (0.30), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.64 (0.80), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.014   0.001   PHE A  87 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.001   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  216)
  hydrogen bonds       : angle       3.50568 (  648)
  SS BOND              : bond        0.00305 (    1)
  SS BOND              : angle       1.19573 (    2)
  covalent geometry    : bond        0.00264 ( 2194)
  covalent geometry    : angle       0.49423 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8683 (t80) cc_final: 0.8414 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.0677
  time to fit residues: 3.5181
Evaluate side-chains
  35 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    0.0670
   chunk 22 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.078078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.067870 restraints weight = 13889.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.069038 restraints weight = 9285.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.069899 restraints weight = 6972.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2195  Z= 0.106
  Angle     :  0.482   5.421   3042  Z= 0.249
  Chirality :  0.039   0.172    394
  Planarity :  0.004   0.040    406
  Dihedral  :  2.967  10.338    367
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 29.81 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.65 (0.47), residues: 350
  helix:  3.07 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.53 (0.79), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 246 
 PHE   0.015   0.001   PHE A  87 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.000   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03208 (  216)
  hydrogen bonds       : angle       3.34161 (  648)
  SS BOND              : bond        0.00484 (    1)
  SS BOND              : angle       0.92242 (    2)
  covalent geometry    : bond        0.00208 ( 2194)
  covalent geometry    : angle       0.48188 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8710 (t80) cc_final: 0.8413 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0689
  time to fit residues: 3.4281
Evaluate side-chains
  35 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    0.0000
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0970
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5582

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.078482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.068310 restraints weight = 13729.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.069482 restraints weight = 9260.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.070296 restraints weight = 6983.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   2195  Z= 0.104
  Angle     :  0.481   5.281   3042  Z= 0.248
  Chirality :  0.039   0.172    394
  Planarity :  0.004   0.041    406
  Dihedral  :  2.951  10.455    367
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 29.81 %
    Favored  : 67.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.67 (0.47), residues: 350
  helix:  3.09 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.58 (0.79), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 246 
 PHE   0.016   0.001   PHE A  87 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.000   0.000   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03062 (  216)
  hydrogen bonds       : angle       3.25475 (  648)
  SS BOND              : bond        0.00315 (    1)
  SS BOND              : angle       1.17607 (    2)
  covalent geometry    : bond        0.00211 ( 2194)
  covalent geometry    : angle       0.48042 ( 3040)

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

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

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  700 Ramachandran restraints generated.
    350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8600 (t80) cc_final: 0.8340 (t80)
  outliers start: 3
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0653
  time to fit residues: 3.2651
Evaluate side-chains
  36 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue 1063 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0170
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0050
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.8038

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.076341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.066240 restraints weight = 14095.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.067438 restraints weight = 9205.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.068262 restraints weight = 6859.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.4329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2195  Z= 0.135
  Angle     :  0.507   4.931   3042  Z= 0.267
  Chirality :  0.040   0.165    394
  Planarity :  0.004   0.041    406
  Dihedral  :  3.074  10.338    367
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 29.81 %
    Favored  : 67.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.65 (0.47), residues: 350
  helix:  3.07 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.55 (0.80), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.006   0.001   HIS A 107 
 PHE   0.014   0.001   PHE A  87 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.001   0.001   ARG A 997 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  216)
  hydrogen bonds       : angle       3.48578 (  648)
  SS BOND              : bond        0.00606 (    1)
  SS BOND              : angle       1.56096 (    2)
  covalent geometry    : bond        0.00284 ( 2194)
  covalent geometry    : angle       0.50578 ( 3040)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1099.85 seconds
wall clock time: 19 minutes 51.38 seconds (1191.38 seconds total)