Starting phenix.real_space_refine
on Wed Mar  5 16:13:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xh6_38342/03_2025/8xh6_38342_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xh6_38342/03_2025/8xh6_38342.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xh6_38342/03_2025/8xh6_38342.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xh6_38342/03_2025/8xh6_38342.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xh6_38342/03_2025/8xh6_38342_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xh6_38342/03_2025/8xh6_38342_neut.cif"
  }
  resolution = 3.52
  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=   0.083
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      14      5.16       5
     C    1870      2.51       5
     N     378      2.21       5
     O     372      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2634
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "B"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
  Time building chain proxies: 2.43, per 1000 atoms: 0.92
  Number of scatterers: 2634
  At special positions: 0
  Unit cell: (57.2, 71.76, 70.72, 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      14     16.00
     O     372      8.00
     N     378      7.00
     C    1870      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: 0.62
  Conformation dependent library (CDL) restraints added in 292.9 milliseconds
  

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  600

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      90.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 45
      removed outlier: 4.261A  pdb=" N   LEU A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   TYR A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 4.057A  pdb=" N   VAL A  54 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A  55 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.821A  pdb=" N   LEU A  76 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 99
      removed outlier: 4.399A  pdb=" N   ASN A  99 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 132
      removed outlier: 4.115A  pdb=" N   LEU A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 160
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 3.534A  pdb=" N   THR A 166 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 168 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 44
      removed outlier: 3.734A  pdb=" N   MET B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 72
    Processing helix  chain 'B' and resid 73 through 77
      removed outlier: 3.874A  pdb=" N   LEU B  76 " --> pdb=" O   ARG B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 100
      removed outlier: 4.401A  pdb=" N   ILE B  95 " --> pdb=" O   THR B  91 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ALA B  96 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 133
      removed outlier: 4.065A  pdb=" N   LEU B 107 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU B 118 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY B 121 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 160
      removed outlier: 3.744A  pdb=" N   PHE B 143 " --> pdb=" O   GLN B 139 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE B 144 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   TYR B 159 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 183
      removed outlier: 4.109A  pdb=" N   LEU B 181 " --> pdb=" O   PHE B 177 " (cutoff:3.500A)

    213 hydrogen bonds defined for protein.
    633 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: 0.65

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 703
        1.34 -     1.46: 689
        1.46 -     1.58: 1292
        1.58 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 2708
  Sorted by residual:
  bond pdb=" CA  TRP A 131 "
       pdb=" C   TRP A 131 "
    ideal  model  delta    sigma   weight residual
    1.522  1.499  0.023 1.41e-02 5.03e+03 2.74e+00
  bond pdb=" CG1 ILE B  95 "
       pdb=" CD1 ILE B  95 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.03e+00
  bond pdb=" CG  LEU B  60 "
       pdb=" CD1 LEU B  60 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.69e-01
  bond pdb=" CG  ARG A  74 "
       pdb=" CD  ARG A  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.85e-01
  bond pdb=" N   MET A 184 "
       pdb=" CA  MET A 184 "
    ideal  model  delta    sigma   weight residual
    1.458  1.472 -0.014 1.90e-02 2.77e+03 5.06e-01
  ... (remaining 2703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 3548
        1.23 -     2.47: 121
        2.47 -     3.70: 25
        3.70 -     4.94: 10
        4.94 -     6.17: 4
  Bond angle restraints: 3708
  Sorted by residual:
  angle pdb=" C   LEU A 130 "
        pdb=" N   TRP A 131 "
        pdb=" CA  TRP A 131 "
      ideal   model   delta    sigma   weight residual
     120.60  125.40   -4.80 1.60e+00 3.91e-01 8.99e+00
  angle pdb=" N   ILE B  71 "
        pdb=" CA  ILE B  71 "
        pdb=" C   ILE B  71 "
      ideal   model   delta    sigma   weight residual
     111.58  108.76    2.82 1.06e+00 8.90e-01 7.10e+00
  angle pdb=" C   TRP A 183 "
        pdb=" N   MET A 184 "
        pdb=" CA  MET A 184 "
      ideal   model   delta    sigma   weight residual
     121.70  125.85   -4.15 1.80e+00 3.09e-01 5.31e+00
  angle pdb=" CB  MET A  61 "
        pdb=" CG  MET A  61 "
        pdb=" SD  MET A  61 "
      ideal   model   delta    sigma   weight residual
     112.70  118.32   -5.62 3.00e+00 1.11e-01 3.51e+00
  angle pdb=" C   ILE A 109 "
        pdb=" CA  ILE A 109 "
        pdb=" CB  ILE A 109 "
      ideal   model   delta    sigma   weight residual
     111.97  109.70    2.27 1.28e+00 6.10e-01 3.14e+00
  ... (remaining 3703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 1320
       16.00 -    32.01: 138
       32.01 -    48.01: 31
       48.01 -    64.02: 1
       64.02 -    80.02: 4
  Dihedral angle restraints: 1494
    sinusoidal: 564
      harmonic: 930
  Sorted by residual:
  dihedral pdb=" CB  MET B  89 "
           pdb=" CG  MET B  89 "
           pdb=" SD  MET B  89 "
           pdb=" CE  MET B  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.18  -56.18     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" CB  GLU B 128 "
           pdb=" CG  GLU B 128 "
           pdb=" CD  GLU B 128 "
           pdb=" OE1 GLU B 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.02   80.02     1      3.00e+01 1.11e-03 8.82e+00
  dihedral pdb=" CA  LEU B 174 "
           pdb=" CB  LEU B 174 "
           pdb=" CG  LEU B 174 "
           pdb=" CD1 LEU B 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.71   43.29     3      1.50e+01 4.44e-03 7.78e+00
  ... (remaining 1491 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 219
       0.021 -    0.042: 137
       0.042 -    0.063: 84
       0.063 -    0.084: 27
       0.084 -    0.106: 7
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CA  CYS A  78 "
            pdb=" N   CYS A  78 "
            pdb=" C   CYS A  78 "
            pdb=" CB  CYS A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.78e-01
  chirality pdb=" CA  THR A  91 "
            pdb=" N   THR A  91 "
            pdb=" C   THR A  91 "
            pdb=" CB  THR A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.43    0.09 2.00e-01 2.50e+01 2.20e-01
  chirality pdb=" CG  LEU A  60 "
            pdb=" CB  LEU A  60 "
            pdb=" CD1 LEU A  60 "
            pdb=" CD2 LEU A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.68    0.09 2.00e-01 2.50e+01 2.03e-01
  ... (remaining 471 not shown)

  Planarity restraints: 402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  74 "   -0.102 9.50e-02 1.11e+02   4.62e-02 1.74e+00
        pdb=" NE  ARG A  74 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  74 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  74 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  74 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  78 "    0.015 5.00e-02 4.00e+02   2.32e-02 8.59e-01
        pdb=" N   PRO B  79 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO B  79 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B  79 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  78 "   -0.015 5.00e-02 4.00e+02   2.23e-02 7.95e-01
        pdb=" N   PRO A  79 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO A  79 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A  79 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 399 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 919
        2.90 -     3.40: 2794
        3.40 -     3.90: 4364
        3.90 -     4.40: 4625
        4.40 -     4.90: 7627
  Nonbonded interactions: 20329
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  99 "
            pdb=" N   LEU B 100 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" O   ASN B  46 "
            pdb=" ND2 ASN B 163 "
     model   vdw
     2.406 3.120
  nonbonded pdb=" O   THR A  48 "
            pdb=" OG1 THR A  48 "
     model   vdw
     2.460 3.040
  nonbonded pdb=" O   PHE B  70 "
            pdb=" NE  ARG B  74 "
     model   vdw
     2.590 3.120
  nonbonded pdb=" OG  SER B  45 "
            pdb=" N   ASN B  46 "
     model   vdw
     2.616 3.120
  ... (remaining 20324 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.150
  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:                     11.460
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
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   0.040   2708  Z= 0.200
  Angle     :  0.586   6.169   3708  Z= 0.297
  Chirality :  0.036   0.106    474
  Planarity :  0.003   0.046    402
  Dihedral  : 14.079  80.022    894
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.24 (0.47), residues: 318
  helix:  1.16 (0.31), residues: 284
  sheet:  None (None), residues: 0
  loop : -1.56 (1.07), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 164 
 HIS   0.001   0.001   HIS A 101 
 PHE   0.011   0.001   PHE A  72 
 TYR   0.007   0.001   TYR A 159 
 ARG   0.012   0.001   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  161 GLN cc_start: 0.6670 (mt0) cc_final: 0.6451 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1389
  time to fit residues: 6.4826
Evaluate side-chains
  32 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0170
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.4036 r_free = 0.4036 target = 0.174909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147102 restraints weight = 3152.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.151066 restraints weight = 1893.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.153420 restraints weight = 1383.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2708  Z= 0.189
  Angle     :  0.523   5.791   3708  Z= 0.247
  Chirality :  0.034   0.096    474
  Planarity :  0.003   0.024    402
  Dihedral  :  3.757  10.372    336
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 10.51 %
    Favored  : 88.77 %
  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:  1.69 (0.46), residues: 318
  helix:  1.42 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.47 (1.15), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 131 
 HIS   0.001   0.001   HIS A 101 
 PHE   0.012   0.001   PHE A  38 
 TYR   0.005   0.001   TYR B 125 
 ARG   0.006   0.001   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  161 GLN cc_start: 0.6808 (mt0) cc_final: 0.6499 (mt0)
REVERT: B  184 MET cc_start: 0.5713 (tpp) cc_final: 0.5438 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1312
  time to fit residues: 7.0110
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:    0.0670
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.174658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.146343 restraints weight = 3127.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.150288 restraints weight = 1892.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.152890 restraints weight = 1388.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2708  Z= 0.174
  Angle     :  0.487   5.440   3708  Z= 0.231
  Chirality :  0.034   0.097    474
  Planarity :  0.003   0.029    402
  Dihedral  :  3.626  10.885    336
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.13 %
    Favored  : 83.70 %
  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:  2.07 (0.46), residues: 318
  helix:  1.68 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.43 (1.13), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 131 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.007   0.001   PHE A 177 
 TYR   0.007   0.001   TYR A 125 
 ARG   0.005   0.001   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  161 GLN cc_start: 0.6774 (mt0) cc_final: 0.6495 (mt0)
REVERT: B  141 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7799 (mm)
  outliers start: 6
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1429
  time to fit residues: 7.0778
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.174279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.146129 restraints weight = 3126.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.150177 restraints weight = 1873.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.152759 restraints weight = 1367.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2708  Z= 0.159
  Angle     :  0.469   5.931   3708  Z= 0.224
  Chirality :  0.033   0.098    474
  Planarity :  0.002   0.026    402
  Dihedral  :  3.588  10.781    336
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.93 %
    Favored  : 77.90 %
  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:  2.34 (0.46), residues: 318
  helix:  1.84 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.18 (1.21), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  39 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.007   0.001   PHE A 177 
 TYR   0.007   0.001   TYR A 125 
 ARG   0.002   0.000   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7751 (tt)
REVERT: A  129 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7320 (mm)
REVERT: B  141 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: B  184 MET cc_start: 0.6263 (tpp) cc_final: 0.5481 (mmt)
  outliers start: 6
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1451
  time to fit residues: 7.0334
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0010
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.3904

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.174905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.146608 restraints weight = 3118.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.150659 restraints weight = 1875.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.153252 restraints weight = 1368.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2708  Z= 0.143
  Angle     :  0.466   7.544   3708  Z= 0.218
  Chirality :  0.033   0.099    474
  Planarity :  0.002   0.026    402
  Dihedral  :  3.487  10.467    336
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.29 %
    Favored  : 76.81 %
  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:  2.66 (0.46), residues: 318
  helix:  2.06 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.10 (1.20), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  39 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.006   0.001   PHE A 177 
 TYR   0.006   0.001   TYR A 125 
 ARG   0.002   0.000   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7662 (tt)
REVERT: A  159 TYR cc_start: 0.6583 (m-10) cc_final: 0.6312 (m-80)
REVERT: B  141 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7833 (mm)
REVERT: B  184 MET cc_start: 0.6344 (tpp) cc_final: 0.5272 (mmt)
  outliers start: 8
  outliers final: 4
  residues processed: 37
  average time/residue: 0.1456
  time to fit residues: 6.6794
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.171036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142159 restraints weight = 3242.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.146281 restraints weight = 1947.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.148764 restraints weight = 1421.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2708  Z= 0.208
  Angle     :  0.526   7.315   3708  Z= 0.241
  Chirality :  0.034   0.103    474
  Planarity :  0.002   0.027    402
  Dihedral  :  3.589  11.104    336
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.65 %
    Favored  : 76.09 %
  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:  2.55 (0.46), residues: 318
  helix:  1.96 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.90 (1.23), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 131 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.007   0.001   PHE A 177 
 TYR   0.003   0.001   TYR B  41 
 ARG   0.001   0.000   ARG B  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B  141 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7878 (mm)
REVERT: B  184 MET cc_start: 0.6062 (tpp) cc_final: 0.5323 (mmt)
  outliers start: 9
  outliers final: 3
  residues processed: 43
  average time/residue: 0.1657
  time to fit residues: 8.6560
Evaluate side-chains
  36 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.169432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.140268 restraints weight = 3298.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.144339 restraints weight = 1976.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.146968 restraints weight = 1450.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2708  Z= 0.226
  Angle     :  0.580   9.043   3708  Z= 0.262
  Chirality :  0.035   0.103    474
  Planarity :  0.003   0.048    402
  Dihedral  :  3.703  11.164    336
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 22.10 %
    Favored  : 74.64 %
  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:  2.54 (0.46), residues: 318
  helix:  1.97 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.04 (1.19), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  39 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.008   0.001   PHE A 177 
 TYR   0.003   0.001   TYR B 106 
 ARG   0.013   0.002   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  172 LEU cc_start: 0.7771 (tt) cc_final: 0.7284 (mt)
REVERT: B  141 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: B  147 PHE cc_start: 0.8586 (t80) cc_final: 0.8135 (t80)
  outliers start: 9
  outliers final: 4
  residues processed: 43
  average time/residue: 0.1609
  time to fit residues: 8.4485
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.175018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.145825 restraints weight = 3179.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.149619 restraints weight = 2016.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152098 restraints weight = 1510.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2708  Z= 0.199
  Angle     :  0.576   8.534   3708  Z= 0.255
  Chirality :  0.034   0.101    474
  Planarity :  0.003   0.026    402
  Dihedral  :  3.635  10.585    336
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 23.55 %
    Favored  : 74.64 %
  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:  2.66 (0.46), residues: 318
  helix:  2.05 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.08 (1.17), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 131 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.008   0.001   PHE A 177 
 TYR   0.004   0.001   TYR B  41 
 ARG   0.007   0.001   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  172 LEU cc_start: 0.7783 (tt) cc_final: 0.7303 (mt)
REVERT: B  141 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7910 (mm)
REVERT: B  147 PHE cc_start: 0.8601 (t80) cc_final: 0.8144 (t80)
REVERT: B  184 MET cc_start: 0.5451 (mmt) cc_final: 0.5209 (tpp)
  outliers start: 5
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1579
  time to fit residues: 7.8524
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.175765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.146051 restraints weight = 3248.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149985 restraints weight = 2027.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.152633 restraints weight = 1508.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2708  Z= 0.182
  Angle     :  0.553   8.806   3708  Z= 0.248
  Chirality :  0.034   0.101    474
  Planarity :  0.002   0.026    402
  Dihedral  :  3.575  10.292    336
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.83 %
    Favored  : 75.00 %
  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:  2.74 (0.46), residues: 318
  helix:  2.10 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.98 (1.18), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 131 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.007   0.001   PHE A 177 
 TYR   0.004   0.001   TYR B  41 
 ARG   0.008   0.001   ARG A  74 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.337 
Fit side-chains
REVERT: B  141 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7913 (mm)
REVERT: B  147 PHE cc_start: 0.8587 (t80) cc_final: 0.8126 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1605
  time to fit residues: 8.2074
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0270
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.171146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142186 restraints weight = 3209.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.146332 restraints weight = 1926.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148946 restraints weight = 1407.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2708  Z= 0.165
  Angle     :  0.576   9.647   3708  Z= 0.251
  Chirality :  0.034   0.099    474
  Planarity :  0.002   0.026    402
  Dihedral  :  3.515  10.202    336
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 24.28 %
    Favored  : 73.91 %
  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: 318
  helix:  2.17 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.91 (1.19), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 131 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.007   0.001   PHE A 177 
 TYR   0.004   0.001   TYR B  41 
 ARG   0.003   0.001   ARG A 132 

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B  141 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7932 (mm)
REVERT: B  147 PHE cc_start: 0.8551 (t80) cc_final: 0.8157 (t80)
REVERT: B  184 MET cc_start: 0.5958 (tpp) cc_final: 0.5187 (mmm)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.1723
  time to fit residues: 7.9336
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.170097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.140912 restraints weight = 3158.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.144922 restraints weight = 1935.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147501 restraints weight = 1430.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2708  Z= 0.200
  Angle     :  0.591   9.472   3708  Z= 0.258
  Chirality :  0.034   0.101    474
  Planarity :  0.002   0.028    402
  Dihedral  :  3.562  10.442    336
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 24.28 %
    Favored  : 73.55 %
  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:  2.80 (0.46), residues: 318
  helix:  2.13 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.88 (1.19), residues: 30

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 131 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.008   0.001   PHE A 177 
 TYR   0.004   0.001   TYR B  41 
 ARG   0.003   0.000   ARG A 132 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1190.76 seconds
wall clock time: 21 minutes 8.94 seconds (1268.94 seconds total)