Starting phenix.real_space_refine
on Wed Sep 17 02:59:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ku5_23034/09_2025/7ku5_23034.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ku5_23034/09_2025/7ku5_23034.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ku5_23034/09_2025/7ku5_23034.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ku5_23034/09_2025/7ku5_23034.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ku5_23034/09_2025/7ku5_23034.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ku5_23034/09_2025/7ku5_23034.map"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.153
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      3      5.21       5
     S       1      5.16       5
     C     512      2.51       5
     N     125      2.21       5
     O     109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 750
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "O"
      Number of atoms: 655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 655
          Classifications: {'peptide': 88}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 81}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "O"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 95
          Unusual residues: {'BCR': 1, 'CLA': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 195
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 3, 'CLA:plan-6': 3, 'BCR:plan-2': 1, 'BCR:plan-3': 1, 'BCR:plan-4': 1, 'BCR:plan-5': 1, 'BCR:plan-6': 1, 'BCR:plan-7': 1, 'BCR:plan-8': 1}
          Unresolved non-hydrogen planarities: 91
  Time building chain proxies: 0.46, per 1000 atoms: 0.61
  Number of scatterers: 750
  At special positions: 0
  Unit cell: (52, 35.36, 62.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       1     16.00
     Mg      3     11.99
     O     109      8.00
     N     125      7.00
     C     512      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: 0.24
  Conformation dependent library (CDL) restraints added in 34.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  150

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 0 sheets defined
      56.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.02
  Creating SS restraints...
    Processing helix  chain 'O' and resid 65 through 73
    Processing helix  chain 'O' and resid 83 through 87
      removed outlier: 4.109A  pdb=" N   SER O  87 " --> pdb=" O   ASN O  84 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 95 through 101
      removed outlier: 3.623A  pdb=" N   GLU O  99 " --> pdb=" O   SER O  95 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 112 through 128
      removed outlier: 4.374A  pdb=" N   TRP O 116 " --> pdb=" O   PRO O 112 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL O 118 " --> pdb=" O   TRP O 114 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   VAL O 122 " --> pdb=" O   VAL O 118 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 129 through 140
      removed outlier: 3.503A  pdb=" N   ILE O 133 " --> pdb=" O   THR O 129 " (cutoff:3.500A)

    25 hydrogen bonds defined for protein.
    72 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: 0.08

  Time building geometry restraints manager: 0.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 335
        1.40 -     1.57: 450
        1.57 -     1.75: 0
        1.75 -     1.92: 2
        1.92 -     2.09: 12
  Bond restraints: 799
  Sorted by residual:
  bond pdb=" C   GLY O 106 "
       pdb=" N   PRO O 107 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.93e+00
  bond pdb=" N   THR O 105 "
       pdb=" CA  THR O 105 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 1.48e-02 4.57e+03 3.42e+00
  bond pdb=" N   TRP O 114 "
       pdb=" CA  TRP O 114 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.29e-02 6.01e+03 3.33e+00
  bond pdb=" C25 BCR O 301 "
       pdb=" C30 BCR O 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.496  0.036 2.00e-02 2.50e+03 3.16e+00
  bond pdb=" CB  TRP O 114 "
       pdb=" CG  TRP O 114 "
    ideal  model  delta    sigma   weight residual
    1.498  1.452  0.046 3.10e-02 1.04e+03 2.25e+00
  ... (remaining 794 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 1069
        2.51 -     5.03: 50
        5.03 -     7.54: 9
        7.54 -    10.06: 4
       10.06 -    12.57: 1
  Bond angle restraints: 1133
  Sorted by residual:
  angle pdb=" C   PRO O 104 "
        pdb=" N   THR O 105 "
        pdb=" CA  THR O 105 "
      ideal   model   delta    sigma   weight residual
     122.61  129.47   -6.86 1.56e+00 4.11e-01 1.93e+01
  angle pdb=" C   TRP O 114 "
        pdb=" CA  TRP O 114 "
        pdb=" CB  TRP O 114 "
      ideal   model   delta    sigma   weight residual
     110.42  102.99    7.43 1.99e+00 2.53e-01 1.39e+01
  angle pdb=" CA  LEU O  91 "
        pdb=" CB  LEU O  91 "
        pdb=" CG  LEU O  91 "
      ideal   model   delta    sigma   weight residual
     116.30  128.87  -12.57 3.50e+00 8.16e-02 1.29e+01
  angle pdb=" N   TRP O 114 "
        pdb=" CA  TRP O 114 "
        pdb=" CB  TRP O 114 "
      ideal   model   delta    sigma   weight residual
     110.49  116.45   -5.96 1.69e+00 3.50e-01 1.24e+01
  angle pdb=" N   TRP O 114 "
        pdb=" CA  TRP O 114 "
        pdb=" C   TRP O 114 "
      ideal   model   delta    sigma   weight residual
     110.80  118.02   -7.22 2.13e+00 2.20e-01 1.15e+01
  ... (remaining 1128 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 332
       17.20 -    34.39: 36
       34.39 -    51.59: 5
       51.59 -    68.79: 0
       68.79 -    85.98: 1
  Dihedral angle restraints: 374
    sinusoidal: 136
      harmonic: 238
  Sorted by residual:
  dihedral pdb=" CA  GLY O 106 "
           pdb=" C   GLY O 106 "
           pdb=" N   PRO O 107 "
           pdb=" CA  PRO O 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.26  -24.74     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  TRP O  74 "
           pdb=" C   TRP O  74 "
           pdb=" N   LEU O  75 "
           pdb=" CA  LEU O  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  PHE O  92 "
           pdb=" C   PHE O  92 "
           pdb=" N   LEU O  93 "
           pdb=" CA  LEU O  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.00   18.00     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 49
       0.046 -    0.091: 33
       0.091 -    0.137: 10
       0.137 -    0.182: 2
       0.182 -    0.228: 3
  Chirality restraints: 97
  Sorted by residual:
  chirality pdb=" CA  TRP O 114 "
            pdb=" N   TRP O 114 "
            pdb=" C   TRP O 114 "
            pdb=" CB  TRP O 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  LEU O  91 "
            pdb=" N   LEU O  91 "
            pdb=" C   LEU O  91 "
            pdb=" CB  LEU O  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.32e-01
  chirality pdb=" CA  THR O 105 "
            pdb=" N   THR O 105 "
            pdb=" C   THR O 105 "
            pdb=" CB  THR O 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.57e-01
  ... (remaining 94 not shown)

  Planarity restraints: 153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" ND  CLA O 201 "    0.064 2.00e-02 2.50e+03   4.55e-02 3.10e+01
        pdb=" C1A CLA O 201 "   -0.028 2.00e-02 2.50e+03
        pdb=" C3D CLA O 201 "   -0.045 2.00e-02 2.50e+03
        pdb=" C4D CLA O 201 "   -0.039 2.00e-02 2.50e+03
        pdb=" CBD CLA O 201 "    0.061 2.00e-02 2.50e+03
        pdb=" CHA CLA O 201 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP O 114 "    0.037 2.00e-02 2.50e+03   2.78e-02 1.93e+01
        pdb=" CG  TRP O 114 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD1 TRP O 114 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP O 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP O 114 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP O 114 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP O 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP O 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP O 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP O 114 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1A CLA O 203 "   -0.019 2.00e-02 2.50e+03   3.56e-02 1.90e+01
        pdb=" C2A CLA O 203 "    0.058 2.00e-02 2.50e+03
        pdb=" C4A CLA O 203 "   -0.032 2.00e-02 2.50e+03
        pdb=" CHA CLA O 203 "   -0.023 2.00e-02 2.50e+03
        pdb=" NA  CLA O 203 "   -0.026 2.00e-02 2.50e+03
        pdb="MG   CLA O 203 "    0.041 2.00e-02 2.50e+03
  ... (remaining 150 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 252
        2.92 -     3.41: 653
        3.41 -     3.91: 1118
        3.91 -     4.40: 1191
        4.40 -     4.90: 1854
  Nonbonded interactions: 5068
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG O  61 "
            pdb=" OE1 GLN O 132 "
     model   vdw
     2.420 3.120
  nonbonded pdb=" NZ  LYS O 136 "
            pdb=" OD2 ASP O 140 "
     model   vdw
     2.502 3.120
  nonbonded pdb=" O   LEU O  75 "
            pdb=" OG  SER O  79 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" O   LEU O  91 "
            pdb=" N   SER O  95 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" O   ASP O  63 "
            pdb=" N   SER O  65 "
     model   vdw
     2.582 3.120
  ... (remaining 5063 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:             1.110
  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:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     2.520
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
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      :  0.006   0.052    799  Z= 0.306
  Angle     :  1.290  12.573   1133  Z= 0.648
  Chirality :  0.068   0.228     97
  Planarity :  0.013   0.066    153
  Dihedral  : 14.852  85.984    224
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.79 %
    Favored  : 87.21 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.41 (0.71), residues: 86
  helix: -4.07 (0.40), residues: 40
  sheet:  None (None), residues: 0
  loop : -3.17 (0.90), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.008   ARG O  62 
 TYR   0.008   0.002   TYR O 142 
 PHE   0.022   0.002   PHE O  92 
 TRP   0.073   0.003   TRP O 114 
 HIS   0.002   0.001   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 (  799)
  covalent geometry    : angle       1.29023 ( 1133)
  hydrogen bonds       : bond        0.30507 (   25)
  hydrogen bonds       : angle      12.13713 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.026 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0685
  time to fit residues: 1.1329
Evaluate side-chains
  12 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.9485

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.178733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.167723 restraints weight = 1641.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.170095 restraints weight = 942.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.171567 restraints weight = 644.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.172692 restraints weight = 492.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.173347 restraints weight = 397.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046    799  Z= 0.207
  Angle     :  0.766   6.362   1133  Z= 0.380
  Chirality :  0.053   0.157     97
  Planarity :  0.007   0.054    153
  Dihedral  :  7.104  23.742     99
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.63 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.00 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.25 (0.83), residues: 86
  helix: -2.70 (0.61), residues: 45
  sheet:  None (None), residues: 0
  loop : -2.93 (1.04), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O 138 
 TYR   0.006   0.002   TYR O 142 
 PHE   0.016   0.002   PHE O  92 
 TRP   0.016   0.002   TRP O 116 
 HIS   0.002   0.001   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (  799)
  covalent geometry    : angle       0.76561 ( 1133)
  hydrogen bonds       : bond        0.04086 (   25)
  hydrogen bonds       : angle       6.78446 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.033 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 16
  average time/residue: 0.0524
  time to fit residues: 0.9378
Evaluate side-chains
  15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   75 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    1.0983

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.177793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.167223 restraints weight = 1564.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.169596 restraints weight = 826.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.171131 restraints weight = 530.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.172054 restraints weight = 386.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172799 restraints weight = 311.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026    799  Z= 0.136
  Angle     :  0.656   6.266   1133  Z= 0.320
  Chirality :  0.048   0.146     97
  Planarity :  0.006   0.045    153
  Dihedral  :  6.645  21.787     99
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.79 %
    Favored  : 87.21 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  :  8.33 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.56 (0.86), residues: 86
  helix: -1.89 (0.63), residues: 45
  sheet:  None (None), residues: 0
  loop : -2.92 (1.09), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O  61 
 TYR   0.005   0.001   TYR O 142 
 PHE   0.015   0.001   PHE O  92 
 TRP   0.008   0.001   TRP O  74 
 HIS   0.000   0.000   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (  799)
  covalent geometry    : angle       0.65649 ( 1133)
  hydrogen bonds       : bond        0.03319 (   25)
  hydrogen bonds       : angle       5.88151 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.026 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 12
  average time/residue: 0.0231
  time to fit residues: 0.3570
Evaluate side-chains
  13 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   75 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0270
   chunk 3 optimal weight:    8.9990
   chunk 4 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5553

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.176751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.167286 restraints weight = 1612.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.169707 restraints weight = 828.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.171182 restraints weight = 518.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.172149 restraints weight = 361.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.172770 restraints weight = 275.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018    799  Z= 0.105
  Angle     :  0.595   6.011   1133  Z= 0.286
  Chirality :  0.047   0.118     97
  Planarity :  0.006   0.043    153
  Dihedral  :  6.171  18.354     99
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  :  8.33 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.90), residues: 86
  helix: -1.05 (0.70), residues: 45
  sheet:  None (None), residues: 0
  loop : -2.94 (1.08), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O  61 
 TYR   0.002   0.001   TYR O 142 
 PHE   0.012   0.001   PHE O  92 
 TRP   0.007   0.001   TRP O  74 
 HIS   0.000   0.000   HIS O 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (  799)
  covalent geometry    : angle       0.59461 ( 1133)
  hydrogen bonds       : bond        0.02746 (   25)
  hydrogen bonds       : angle       5.41918 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.027 
Fit side-chains
REVERT: O  142 TYR cc_start: 0.7668 (m-80) cc_final: 0.7181 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0209
  time to fit residues: 0.3747
Evaluate side-chains
  14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   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 = 0.4092 r_free = 0.4092 target = 0.175776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.166604 restraints weight = 1602.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.168988 restraints weight = 808.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.170423 restraints weight = 496.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.171365 restraints weight = 345.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.171365 restraints weight = 261.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018    799  Z= 0.109
  Angle     :  0.602   6.028   1133  Z= 0.286
  Chirality :  0.049   0.168     97
  Planarity :  0.006   0.042    153
  Dihedral  :  6.108  19.665     99
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.67 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.93), residues: 86
  helix: -0.61 (0.72), residues: 46
  sheet:  None (None), residues: 0
  loop : -2.83 (1.11), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O  61 
 TYR   0.004   0.001   TYR O 142 
 PHE   0.010   0.001   PHE O  92 
 TRP   0.009   0.001   TRP O  74 
 HIS   0.001   0.000   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (  799)
  covalent geometry    : angle       0.60185 ( 1133)
  hydrogen bonds       : bond        0.02776 (   25)
  hydrogen bonds       : angle       5.20302 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.027 
Fit side-chains
REVERT: O  114 TRP cc_start: 0.6962 (m-90) cc_final: 0.6517 (m-10)
REVERT: O  142 TYR cc_start: 0.7689 (m-80) cc_final: 0.7221 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 16
  average time/residue: 0.0222
  time to fit residues: 0.4489
Evaluate side-chains
  15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   82 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6805

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.179316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.171045 restraints weight = 1683.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.173304 restraints weight = 827.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.174590 restraints weight = 492.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175425 restraints weight = 335.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.175857 restraints weight = 253.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020    799  Z= 0.108
  Angle     :  0.578   5.893   1133  Z= 0.279
  Chirality :  0.047   0.136     97
  Planarity :  0.005   0.041    153
  Dihedral  :  5.963  19.194     99
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.00 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.92), residues: 86
  helix: -0.49 (0.70), residues: 46
  sheet:  None (None), residues: 0
  loop : -2.75 (1.12), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O  61 
 TYR   0.003   0.001   TYR O 142 
 PHE   0.008   0.001   PHE O  92 
 TRP   0.007   0.001   TRP O  74 
 HIS   0.000   0.000   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (  799)
  covalent geometry    : angle       0.57827 ( 1133)
  hydrogen bonds       : bond        0.02767 (   25)
  hydrogen bonds       : angle       4.99102 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.028 
Fit side-chains
REVERT: O  114 TRP cc_start: 0.6923 (m-90) cc_final: 0.6504 (m-10)
REVERT: O  142 TYR cc_start: 0.7646 (m-80) cc_final: 0.7309 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 16
  average time/residue: 0.0230
  time to fit residues: 0.4645
Evaluate side-chains
  16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   75 LEU
Chi-restraints excluded: chain O residue   82 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.167804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.157937 restraints weight = 1535.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.160348 restraints weight = 750.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.161631 restraints weight = 458.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.162849 restraints weight = 336.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.163545 restraints weight = 250.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048    799  Z= 0.199
  Angle     :  0.673   6.133   1133  Z= 0.342
  Chirality :  0.054   0.133     97
  Planarity :  0.006   0.039    153
  Dihedral  :  6.612  18.168     99
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.33 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.89), residues: 86
  helix: -0.95 (0.69), residues: 46
  sheet:  None (None), residues: 0
  loop : -2.90 (1.07), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O  62 
 TYR   0.009   0.003   TYR O 142 
 PHE   0.015   0.002   PHE O 135 
 TRP   0.009   0.002   TRP O 116 
 HIS   0.001   0.000   HIS O 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (  799)
  covalent geometry    : angle       0.67301 ( 1133)
  hydrogen bonds       : bond        0.04006 (   25)
  hydrogen bonds       : angle       5.58915 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.027 
Fit side-chains
REVERT: O  114 TRP cc_start: 0.7365 (m-90) cc_final: 0.4617 (p-90)
REVERT: O  142 TYR cc_start: 0.7907 (m-80) cc_final: 0.7410 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0265
  time to fit residues: 0.4597
Evaluate side-chains
  14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   82 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   overall best weight:    2.1235

-------------------------------------------------------------------------------
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 = 0.4065 r_free = 0.4065 target = 0.171699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.162396 restraints weight = 1483.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.164621 restraints weight = 727.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.166097 restraints weight = 446.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.166935 restraints weight = 313.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.167568 restraints weight = 247.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041    799  Z= 0.189
  Angle     :  0.700   5.755   1133  Z= 0.353
  Chirality :  0.051   0.130     97
  Planarity :  0.006   0.040    153
  Dihedral  :  6.410  16.648     99
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.63 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.67 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.00 (0.87), residues: 86
  helix: -1.07 (0.67), residues: 45
  sheet:  None (None), residues: 0
  loop : -3.14 (1.05), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O  62 
 TYR   0.005   0.002   TYR O 142 
 PHE   0.009   0.002   PHE O 135 
 TRP   0.012   0.001   TRP O  74 
 HIS   0.001   0.001   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (  799)
  covalent geometry    : angle       0.70048 ( 1133)
  hydrogen bonds       : bond        0.03897 (   25)
  hydrogen bonds       : angle       5.60870 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.027 
Fit side-chains
REVERT: O  114 TRP cc_start: 0.7173 (m-90) cc_final: 0.4725 (p-90)
REVERT: O  142 TYR cc_start: 0.7887 (m-80) cc_final: 0.7357 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 15
  average time/residue: 0.0268
  time to fit residues: 0.4967
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue  100 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.6230

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.177847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.169233 restraints weight = 1570.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.171493 restraints weight = 764.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.172818 restraints weight = 445.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.173482 restraints weight = 305.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.174006 restraints weight = 238.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.5053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024    799  Z= 0.111
  Angle     :  0.587   5.603   1133  Z= 0.292
  Chirality :  0.046   0.115     97
  Planarity :  0.006   0.040    153
  Dihedral  :  6.135  16.999     99
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.33 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.27 (0.95), residues: 86
  helix: -0.42 (0.74), residues: 46
  sheet:  None (None), residues: 0
  loop : -2.91 (1.12), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O 138 
 TYR   0.001   0.000   TYR O 142 
 PHE   0.009   0.001   PHE O  92 
 TRP   0.012   0.001   TRP O  74 
 HIS   0.001   0.000   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (  799)
  covalent geometry    : angle       0.58727 ( 1133)
  hydrogen bonds       : bond        0.03078 (   25)
  hydrogen bonds       : angle       5.42525 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.034 
Fit side-chains
REVERT: O  114 TRP cc_start: 0.6962 (m-90) cc_final: 0.4626 (p-90)
REVERT: O  142 TYR cc_start: 0.7759 (m-80) cc_final: 0.7291 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 17
  average time/residue: 0.0279
  time to fit residues: 0.5854
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   82 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.2980
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0170
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.181819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.173956 restraints weight = 1464.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.175811 restraints weight = 787.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.176980 restraints weight = 501.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.177867 restraints weight = 365.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.178157 restraints weight = 278.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.5027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025    799  Z= 0.105
  Angle     :  0.582   5.695   1133  Z= 0.280
  Chirality :  0.044   0.117     97
  Planarity :  0.005   0.040    153
  Dihedral  :  5.617  17.956     99
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.33 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.99), residues: 86
  helix: -0.88 (0.71), residues: 51
  sheet:  None (None), residues: 0
  loop : -1.89 (1.36), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O 138 
 TYR   0.002   0.000   TYR O 142 
 PHE   0.008   0.001   PHE O  92 
 TRP   0.011   0.001   TRP O  74 
 HIS   0.000   0.000   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (  799)
  covalent geometry    : angle       0.58208 ( 1133)
  hydrogen bonds       : bond        0.03227 (   25)
  hydrogen bonds       : angle       5.21190 (   72)

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

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

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  172 Ramachandran restraints generated.
    86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.027 
Fit side-chains
REVERT: O  114 TRP cc_start: 0.6690 (m-90) cc_final: 0.4699 (p-90)
REVERT: O  142 TYR cc_start: 0.7495 (m-80) cc_final: 0.7140 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 17
  average time/residue: 0.0235
  time to fit residues: 0.4976
Evaluate side-chains
  17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   82 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 8
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   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 = 0.4123 r_free = 0.4123 target = 0.177203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.167673 restraints weight = 1404.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.169870 restraints weight = 731.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.171328 restraints weight = 455.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.172292 restraints weight = 320.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.172729 restraints weight = 246.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029    799  Z= 0.117
  Angle     :  0.594   5.711   1133  Z= 0.299
  Chirality :  0.045   0.117     97
  Planarity :  0.006   0.040    153
  Dihedral  :  5.610  18.193     99
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.63 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 21.67 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (1.00), residues: 86
  helix: -0.77 (0.73), residues: 51
  sheet:  None (None), residues: 0
  loop : -1.87 (1.35), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O  61 
 TYR   0.002   0.001   TYR O 142 
 PHE   0.010   0.001   PHE O  92 
 TRP   0.009   0.001   TRP O  74 
 HIS   0.001   0.000   HIS O 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (  799)
  covalent geometry    : angle       0.59397 ( 1133)
  hydrogen bonds       : bond        0.02865 (   25)
  hydrogen bonds       : angle       5.05637 (   72)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 414.12 seconds
wall clock time: 8 minutes 38.85 seconds (518.85 seconds total)