Starting phenix.real_space_refine
on Wed Sep 17 03:00:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9as7_43807/09_2025/9as7_43807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9as7_43807/09_2025/9as7_43807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9as7_43807/09_2025/9as7_43807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9as7_43807/09_2025/9as7_43807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9as7_43807/09_2025/9as7_43807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9as7_43807/09_2025/9as7_43807.cif"
  }
  resolution = 2.72
  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=  -0.003 sd=   0.140
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    1341      2.51       5
     N     303      2.21       5
     O     329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 1987
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 1972
          Classifications: {'peptide': 262}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 9, 'TRANS': 252}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 85
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 59
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'91Q': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.94, per 1000 atoms: 0.47
  Number of scatterers: 1987
  At special positions: 0
  Unit cell: (60.72, 69.52, 66, 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     329      8.00
     N     303      7.00
     C    1341      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 148 " - pdb=" SG  CYS A 227 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 87.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  504

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 1 sheets defined
      90.1% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 81 through 102
      removed outlier: 3.548A  pdb=" N   GLU A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 106
      removed outlier: 3.830A  pdb=" N   GLN A 106 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 106'
    Processing helix  chain 'A' and resid 107 through 127
      removed outlier: 3.634A  pdb=" N   PHE A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 137
    Processing helix  chain 'A' and resid 146 through 179
      removed outlier: 4.219A  pdb=" N   VAL A 150 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 188 through 208
    Processing helix  chain 'A' and resid 208 through 215
      removed outlier: 4.157A  pdb=" N   VAL A 212 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 215 " --> pdb=" O   PRO A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 220
    Processing helix  chain 'A' and resid 231 through 241
      removed outlier: 3.698A  pdb=" N   SER A 239 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 261
    Processing helix  chain 'A' and resid 314 through 349
      removed outlier: 3.524A  pdb=" N   GLU A 318 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
      removed outlier: 3.613A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 382
      removed outlier: 3.611A  pdb=" N   VAL A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   TRP A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   SER A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   SER A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 370 " (cutoff:3.500A)
      Proline residue:  A 377  - end of helix
    Processing helix  chain 'A' and resid 384 through 392
    Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 223

    164 hydrogen bonds defined for protein.
    486 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: 0.34

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 574
        1.35 -     1.46: 531
        1.46 -     1.58: 908
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 2035
  Sorted by residual:
  bond pdb=" N   ASN A 384 "
       pdb=" CA  ASN A 384 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.33e-02 5.65e+03 6.45e+00
  bond pdb=" C9  91Q A 501 "
       pdb=" O1  91Q A 501 "
    ideal  model  delta    sigma   weight residual
    1.349  1.399 -0.050 2.00e-02 2.50e+03 6.17e+00
  bond pdb=" N   ASN A 110 "
       pdb=" CA  ASN A 110 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.032 1.28e-02 6.10e+03 6.07e+00
  bond pdb=" N   ASP A 172 "
       pdb=" CA  ASP A 172 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.23e-02 6.61e+03 5.92e+00
  bond pdb=" C6  91Q A 501 "
       pdb=" N2  91Q A 501 "
    ideal  model  delta    sigma   weight residual
    1.368  1.323  0.045 2.00e-02 2.50e+03 5.01e+00
  ... (remaining 2030 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 2569
        1.24 -     2.47: 160
        2.47 -     3.71: 38
        3.71 -     4.94: 13
        4.94 -     6.18: 7
  Bond angle restraints: 2787
  Sorted by residual:
  angle pdb=" C   ILE A 237 "
        pdb=" CA  ILE A 237 "
        pdb=" CB  ILE A 237 "
      ideal   model   delta    sigma   weight residual
     112.22  108.09    4.13 1.38e+00 5.25e-01 8.95e+00
  angle pdb=" CA  THR A 381 "
        pdb=" CB  THR A 381 "
        pdb=" OG1 THR A 381 "
      ideal   model   delta    sigma   weight residual
     109.60  105.16    4.44 1.50e+00 4.44e-01 8.75e+00
  angle pdb=" CA  MET A 164 "
        pdb=" CB  MET A 164 "
        pdb=" CG  MET A 164 "
      ideal   model   delta    sigma   weight residual
     114.10  119.83   -5.73 2.00e+00 2.50e-01 8.22e+00
  angle pdb=" CA  ASP A 172 "
        pdb=" CB  ASP A 172 "
        pdb=" CG  ASP A 172 "
      ideal   model   delta    sigma   weight residual
     112.60  115.18   -2.58 1.00e+00 1.00e+00 6.68e+00
  angle pdb=" CA  TYR A 370 "
        pdb=" CB  TYR A 370 "
        pdb=" CG  TYR A 370 "
      ideal   model   delta    sigma   weight residual
     113.90  118.26   -4.36 1.80e+00 3.09e-01 5.86e+00
  ... (remaining 2782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.73: 1084
       22.73 -    45.47: 78
       45.47 -    68.20: 8
       68.20 -    90.93: 0
       90.93 -   113.66: 2
  Dihedral angle restraints: 1172
    sinusoidal: 400
      harmonic: 772
  Sorted by residual:
  dihedral pdb=" C2  91Q A 501 "
           pdb=" C3  91Q A 501 "
           pdb=" N1  91Q A 501 "
           pdb=" C4  91Q A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      73.77  -39.89  113.66     1      3.00e+01 1.11e-03 1.49e+01
  dihedral pdb=" C1  91Q A 501 "
           pdb=" C3  91Q A 501 "
           pdb=" N1  91Q A 501 "
           pdb=" C4  91Q A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     198.00   87.95  110.05     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" CA  PRO A 142 "
           pdb=" C   PRO A 142 "
           pdb=" N   LEU A 143 "
           pdb=" CA  LEU A 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.23  -15.77     0      5.00e+00 4.00e-02 9.95e+00
  ... (remaining 1169 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 217
       0.031 -    0.063: 92
       0.063 -    0.094: 40
       0.094 -    0.126: 4
       0.126 -    0.157: 1
  Chirality restraints: 354
  Sorted by residual:
  chirality pdb=" CA  MET A 164 "
            pdb=" N   MET A 164 "
            pdb=" C   MET A 164 "
            pdb=" CB  MET A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.19e-01
  chirality pdb=" CA  PRO A 209 "
            pdb=" N   PRO A 209 "
            pdb=" C   PRO A 209 "
            pdb=" CB  PRO A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.91e-01
  chirality pdb=" CA  PRO A 129 "
            pdb=" N   PRO A 129 "
            pdb=" C   PRO A 129 "
            pdb=" CB  PRO A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.77e-01
  ... (remaining 351 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 141 "   -0.066 5.00e-02 4.00e+02   9.88e-02 1.56e+01
        pdb=" N   PRO A 142 "    0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO A 142 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 142 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 336 "    0.012 2.00e-02 2.50e+03   1.05e-02 2.74e+00
        pdb=" CG  TRP A 336 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 336 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 336 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 336 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 336 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 336 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 336 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 336 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 336 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 383 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   PHE A 383 "    0.027 2.00e-02 2.50e+03
        pdb=" O   PHE A 383 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN A 384 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 121
        2.74 -     3.28: 2092
        3.28 -     3.82: 3361
        3.82 -     4.36: 3819
        4.36 -     4.90: 6669
  Nonbonded interactions: 16062
  Sorted by model distance:
  nonbonded pdb=" O   SER A 392 "
            pdb=" OG  SER A 392 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   LEU A 382 "
            pdb=" NH1 ARG A 388 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" O   ALA A 161 "
            pdb=" ND1 HIS A 165 "
     model   vdw
     2.477 3.120
  nonbonded pdb=" O   ILE A 249 "
            pdb=" OG1 THR A 253 "
     model   vdw
     2.521 3.040
  nonbonded pdb=" O   THR A 253 "
            pdb=" OG1 THR A 257 "
     model   vdw
     2.563 3.040
  ... (remaining 16057 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  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:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.840
  Find NCS groups from input model:        0.010
  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:           0.010
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
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      :  0.005   0.050   2036  Z= 0.250
  Angle     :  0.792   6.177   2789  Z= 0.447
  Chirality :  0.040   0.157    354
  Planarity :  0.007   0.099    327
  Dihedral  : 16.113 113.662    665
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.15 %
    Favored  : 78.85 %
  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:  1.55 (0.53), residues: 256
  helix:  1.25 (0.35), residues: 215
  sheet:  None (None), residues: 0
  loop :  0.24 (1.11), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 388 
 TYR   0.009   0.001   TYR A 139 
 PHE   0.016   0.001   PHE A 332 
 TRP   0.029   0.002   TRP A 336 
 HIS   0.003   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 2035)
  covalent geometry    : angle       0.79258 ( 2787)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.45270 (    2)
  hydrogen bonds       : bond        0.13892 (  164)
  hydrogen bonds       : angle       6.12270 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.127 
Fit side-chains
  outliers start: 0
  outliers final: 1
  residues processed: 30
  average time/residue: 0.4165
  time to fit residues: 12.9045
Evaluate side-chains
  26 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.188373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.175259 restraints weight = 2196.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 1.32
r_work: 0.3986 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3892 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2036  Z= 0.147
  Angle     :  0.613   7.537   2789  Z= 0.310
  Chirality :  0.041   0.116    354
  Planarity :  0.006   0.082    327
  Dihedral  :  8.265  80.303    278
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.83 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.14 (0.53), residues: 256
  helix:  1.10 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.19 (1.09), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 388 
 TYR   0.015   0.002   TYR A 139 
 PHE   0.012   0.002   PHE A 332 
 TRP   0.014   0.002   TRP A 367 
 HIS   0.003   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 2035)
  covalent geometry    : angle       0.61316 ( 2787)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       0.21206 (    2)
  hydrogen bonds       : bond        0.04537 (  164)
  hydrogen bonds       : angle       4.74484 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  114 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.6215 (ttm)
REVERT: A  318 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7215 (mt-10)
REVERT: A  392 SER cc_start: 0.7038 (t) cc_final: 0.6627 (m)
  outliers start: 5
  outliers final: 1
  residues processed: 32
  average time/residue: 0.4450
  time to fit residues: 14.6435
Evaluate side-chains
  29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  348 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0020
   overall best weight:    0.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.190343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.177336 restraints weight = 2189.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 1.32
r_work: 0.4018 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3923 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2036  Z= 0.113
  Angle     :  0.541   6.264   2789  Z= 0.272
  Chirality :  0.039   0.117    354
  Planarity :  0.005   0.069    327
  Dihedral  :  7.884  78.197    276
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.71 %
    Favored  : 76.92 %
  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:  1.55 (0.53), residues: 256
  helix:  1.39 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.07 (1.10), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 388 
 TYR   0.011   0.001   TYR A 139 
 PHE   0.011   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2035)
  covalent geometry    : angle       0.54155 ( 2787)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       0.03189 (    2)
  hydrogen bonds       : bond        0.03779 (  164)
  hydrogen bonds       : angle       4.47159 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  318 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7179 (mt-10)
REVERT: A  392 SER cc_start: 0.6847 (t) cc_final: 0.6455 (m)
  outliers start: 7
  outliers final: 1
  residues processed: 33
  average time/residue: 0.4042
  time to fit residues: 13.7335
Evaluate side-chains
  28 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0000
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.188784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.175845 restraints weight = 2193.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 1.32
r_work: 0.3997 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3902 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2036  Z= 0.127
  Angle     :  0.569   7.097   2789  Z= 0.286
  Chirality :  0.039   0.120    354
  Planarity :  0.005   0.068    327
  Dihedral  :  7.692  74.980    276
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 19.23 %
    Favored  : 76.92 %
  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:  1.51 (0.53), residues: 256
  helix:  1.36 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.12 (1.09), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 388 
 TYR   0.012   0.001   TYR A 139 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 2035)
  covalent geometry    : angle       0.56967 ( 2787)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.05543 (    2)
  hydrogen bonds       : bond        0.04053 (  164)
  hydrogen bonds       : angle       4.43918 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  114 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6191 (ttm)
REVERT: A  194 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4496 (tt)
REVERT: A  318 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7184 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 34
  average time/residue: 0.4131
  time to fit residues: 14.4612
Evaluate side-chains
  32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4158 r_free = 0.4158 target = 0.187149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.174183 restraints weight = 2185.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 1.31
r_work: 0.3984 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3891 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2036  Z= 0.135
  Angle     :  0.583   7.429   2789  Z= 0.290
  Chirality :  0.040   0.123    354
  Planarity :  0.005   0.065    327
  Dihedral  :  7.672  74.194    276
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.75 %
    Favored  : 76.92 %
  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:  1.43 (0.53), residues: 256
  helix:  1.31 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.20 (1.08), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 388 
 TYR   0.013   0.002   TYR A 139 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2035)
  covalent geometry    : angle       0.58280 ( 2787)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       0.03096 (    2)
  hydrogen bonds       : bond        0.04180 (  164)
  hydrogen bonds       : angle       4.46462 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  114 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.6159 (ttm)
REVERT: A  194 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4524 (tt)
REVERT: A  318 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7227 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 29
  average time/residue: 0.3947
  time to fit residues: 11.8127
Evaluate side-chains
  32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.187732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.175059 restraints weight = 2155.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 1.25
r_work: 0.3992 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3899 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2036  Z= 0.135
  Angle     :  0.581   7.407   2789  Z= 0.291
  Chirality :  0.040   0.139    354
  Planarity :  0.005   0.065    327
  Dihedral  :  7.617  73.400    276
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 17.79 %
    Favored  : 76.92 %
  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:  1.39 (0.52), residues: 256
  helix:  1.28 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.19 (1.07), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 388 
 TYR   0.013   0.002   TYR A 139 
 PHE   0.010   0.001   PHE A 193 
 TRP   0.011   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2035)
  covalent geometry    : angle       0.58091 ( 2787)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.05135 (    2)
  hydrogen bonds       : bond        0.04218 (  164)
  hydrogen bonds       : angle       4.45123 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 25
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  114 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6170 (ttm)
REVERT: A  194 LEU cc_start: 0.4783 (OUTLIER) cc_final: 0.4489 (tt)
REVERT: A  318 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7223 (mt-10)
  outliers start: 11
  outliers final: 7
  residues processed: 33
  average time/residue: 0.3545
  time to fit residues: 12.0902
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.3980
   chunk 0 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4159 r_free = 0.4159 target = 0.187194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.174357 restraints weight = 2152.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 1.30
r_work: 0.3991 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3896 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2036  Z= 0.135
  Angle     :  0.589   7.386   2789  Z= 0.293
  Chirality :  0.040   0.140    354
  Planarity :  0.005   0.063    327
  Dihedral  :  7.590  72.747    276
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.23 %
    Favored  : 76.44 %
  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:  1.38 (0.52), residues: 256
  helix:  1.29 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.26 (1.07), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 388 
 TYR   0.013   0.002   TYR A 139 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.011   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 2035)
  covalent geometry    : angle       0.58884 ( 2787)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       0.06725 (    2)
  hydrogen bonds       : bond        0.04209 (  164)
  hydrogen bonds       : angle       4.46269 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A  114 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6154 (ttm)
REVERT: A  194 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.4464 (tt)
REVERT: A  318 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7218 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 31
  average time/residue: 0.3544
  time to fit residues: 11.2987
Evaluate side-chains
  32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 10 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 = 0.4156 r_free = 0.4156 target = 0.186702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.173860 restraints weight = 2227.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 1.33
r_work: 0.3993 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3900 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2036  Z= 0.147
  Angle     :  0.604   7.645   2789  Z= 0.304
  Chirality :  0.040   0.112    354
  Planarity :  0.005   0.063    327
  Dihedral  :  7.578  72.207    276
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 19.23 %
    Favored  : 75.96 %
  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:  1.21 (0.52), residues: 256
  helix:  1.20 (0.34), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.47 (1.04), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 388 
 TYR   0.014   0.002   TYR A 139 
 PHE   0.015   0.002   PHE A 193 
 TRP   0.012   0.002   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2035)
  covalent geometry    : angle       0.60457 ( 2787)
  SS BOND              : bond        0.00243 (    1)
  SS BOND              : angle       0.07092 (    2)
  hydrogen bonds       : bond        0.04342 (  164)
  hydrogen bonds       : angle       4.50234 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  114 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6150 (ttm)
REVERT: A  194 LEU cc_start: 0.4858 (OUTLIER) cc_final: 0.4566 (tt)
REVERT: A  318 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7213 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 34
  average time/residue: 0.3191
  time to fit residues: 11.1958
Evaluate side-chains
  34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  373 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0070
   chunk 12 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0770
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.190088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.177270 restraints weight = 2160.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 1.31
r_work: 0.4027 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3931 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2036  Z= 0.109
  Angle     :  0.540   6.356   2789  Z= 0.273
  Chirality :  0.039   0.148    354
  Planarity :  0.005   0.059    327
  Dihedral  :  7.343  71.276    276
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.63 %
    Favored  : 75.96 %
  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:  1.81 (0.53), residues: 256
  helix:  1.59 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.20 (1.09), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 388 
 TYR   0.014   0.001   TYR A 153 
 PHE   0.009   0.001   PHE A 332 
 TRP   0.010   0.001   TRP A 367 
 HIS   0.003   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 2035)
  covalent geometry    : angle       0.54014 ( 2787)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       0.13251 (    2)
  hydrogen bonds       : bond        0.03526 (  164)
  hydrogen bonds       : angle       4.28839 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  194 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.4585 (tt)
REVERT: A  318 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7281 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 29
  average time/residue: 0.3582
  time to fit residues: 10.7398
Evaluate side-chains
  30 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0070
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4598

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.189329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.176580 restraints weight = 2214.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 1.31
r_work: 0.4004 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3910 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2036  Z= 0.122
  Angle     :  0.564   6.677   2789  Z= 0.282
  Chirality :  0.039   0.113    354
  Planarity :  0.005   0.061    327
  Dihedral  :  7.300  70.254    276
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 20.67 %
    Favored  : 75.48 %
  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:  1.77 (0.53), residues: 256
  helix:  1.56 (0.34), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.20 (1.09), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 388 
 TYR   0.011   0.001   TYR A 139 
 PHE   0.023   0.001   PHE A 193 
 TRP   0.011   0.001   TRP A 367 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2035)
  covalent geometry    : angle       0.56400 ( 2787)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       0.10291 (    2)
  hydrogen bonds       : bond        0.03783 (  164)
  hydrogen bonds       : angle       4.31990 (  486)

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

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

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  512 Ramachandran restraints generated.
    256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  194 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4598 (tt)
REVERT: A  318 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7282 (mt-10)
REVERT: A  327 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6179 (tt)
  outliers start: 8
  outliers final: 5
  residues processed: 31
  average time/residue: 0.3705
  time to fit residues: 11.8641
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  373 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   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 = 0.4156 r_free = 0.4156 target = 0.186520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.173724 restraints weight = 2190.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 1.30
r_work: 0.3983 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3887 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2036  Z= 0.147
  Angle     :  0.609   7.463   2789  Z= 0.305
  Chirality :  0.041   0.145    354
  Planarity :  0.005   0.062    327
  Dihedral  :  7.465  70.897    276
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.67 %
    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 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:  1.32 (0.52), residues: 256
  helix:  1.28 (0.34), residues: 221
  sheet:  None (None), residues: 0
  loop : -1.43 (1.05), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 388 
 TYR   0.014   0.002   TYR A 139 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.011   0.001   TRP A 367 
 HIS   0.003   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2035)
  covalent geometry    : angle       0.60883 ( 2787)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.07878 (    2)
  hydrogen bonds       : bond        0.04344 (  164)
  hydrogen bonds       : angle       4.47398 (  486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 975.63 seconds
wall clock time: 17 minutes 17.04 seconds (1037.04 seconds total)