Starting phenix.real_space_refine
on Tue Mar  3 11:08:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ul5_26592/03_2026/7ul5_26592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ul5_26592/03_2026/7ul5_26592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2026/7ul5_26592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2026/7ul5_26592.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2026/7ul5_26592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2026/7ul5_26592.map"
  }
  resolution = 3.1
  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=  -0.001 sd=   0.088
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      24      5.16       5
     C    1834      2.51       5
     N     449      2.21       5
     O     466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2773
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2169
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "D"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 604
          Classifications: {'peptide': 86}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'TRANS': 85}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
  Time building chain proxies: 0.60, per 1000 atoms: 0.22
  Number of scatterers: 2773
  At special positions: 0
  Unit cell: (67.3159, 57.9428, 109.069, 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      24     16.00
     O     466      8.00
     N     449      7.00
     C    1834      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  97 " 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: 0.26
  Conformation dependent library (CDL) restraints added in 79.7 milliseconds
  

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  694

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 4 sheets defined
      65.5% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 71
      removed outlier: 3.985A  pdb=" N   ALA A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR A  71 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 105
      removed outlier: 4.245A  pdb=" N   TYR A  81 " --> pdb=" O   ILE A  77 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 112 through 146
      removed outlier: 3.649A  pdb=" N   VAL A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   SER A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ILE A 130 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.940A  pdb=" N   ALA A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LYS A 152 " --> pdb=" O   LYS A 149 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 152'
    Processing helix  chain 'A' and resid 155 through 180
      removed outlier: 3.515A  pdb=" N   ALA A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LYS A 160 " --> pdb=" O   PRO A 156 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   MET A 161 " --> pdb=" O   ARG A 157 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.532A  pdb=" N   ILE A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 238
      removed outlier: 3.627A  pdb=" N   ILE A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE A 233 " --> pdb=" O   LEU A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 282
      removed outlier: 3.531A  pdb=" N   ARG A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
      Proline residue:  A 271  - end of helix
    Processing helix  chain 'A' and resid 288 through 315
      removed outlier: 4.273A  pdb=" N   GLY A 292 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   SER A 305 " --> pdb=" O   THR A 301 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   CYS A 306 " --> pdb=" O   TYR A 302 " (cutoff:3.500A)
      Proline residue:  A 309  - end of helix
      removed outlier: 3.732A  pdb=" N   TYR A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ALA A 313 " --> pdb=" O   PRO A 309 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE A 314 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 328
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 185
    Processing sheet with id=AA2, first strand: chain 'D' and resid 5 through 9
      removed outlier: 3.687A  pdb=" N   SER D  23 " --> pdb=" O   SER D   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 32 through 33
      removed outlier: 3.630A  pdb=" N   ARG D  32 " --> pdb=" O   ARG D 102 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 33
      removed outlier: 3.630A  pdb=" N   ARG D  32 " --> pdb=" O   ARG D 102 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    576 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: 0.36

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 842
        1.34 -     1.46: 637
        1.46 -     1.58: 1320
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 2835
  Sorted by residual:
  bond pdb=" CB  CYS A 306 "
       pdb=" SG  CYS A 306 "
    ideal  model  delta    sigma   weight residual
    1.808  1.769  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" CG  LEU D  33 "
       pdb=" CD1 LEU D  33 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.11e+00
  bond pdb=" CA  LEU A  96 "
       pdb=" C   LEU A  96 "
    ideal  model  delta    sigma   weight residual
    1.525  1.537 -0.012 1.19e-02 7.06e+03 1.10e+00
  bond pdb=" CB  VAL D  80 "
       pdb=" CG2 VAL D  80 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  bond pdb=" CA  ASP D 111 "
       pdb=" CB  ASP D 111 "
    ideal  model  delta    sigma   weight residual
    1.535  1.555 -0.020 2.02e-02 2.45e+03 9.73e-01
  ... (remaining 2830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 3740
        1.59 -     3.18: 106
        3.18 -     4.77: 20
        4.77 -     6.36: 0
        6.36 -     7.95: 1
  Bond angle restraints: 3867
  Sorted by residual:
  angle pdb=" N   PHE A 127 "
        pdb=" CA  PHE A 127 "
        pdb=" C   PHE A 127 "
      ideal   model   delta    sigma   weight residual
     112.68  116.13   -3.45 1.33e+00 5.65e-01 6.71e+00
  angle pdb=" N   ASN A 308 "
        pdb=" CA  ASN A 308 "
        pdb=" C   ASN A 308 "
      ideal   model   delta    sigma   weight residual
     113.16  116.80   -3.64 1.42e+00 4.96e-01 6.57e+00
  angle pdb=" CA  LEU A 105 "
        pdb=" CB  LEU A 105 "
        pdb=" CG  LEU A 105 "
      ideal   model   delta    sigma   weight residual
     116.30  124.25   -7.95 3.50e+00 8.16e-02 5.17e+00
  angle pdb=" CA  ASP D 111 "
        pdb=" CB  ASP D 111 "
        pdb=" CG  ASP D 111 "
      ideal   model   delta    sigma   weight residual
     112.60  114.70   -2.10 1.00e+00 1.00e+00 4.39e+00
  angle pdb=" N   GLN A 126 "
        pdb=" CA  GLN A 126 "
        pdb=" C   GLN A 126 "
      ideal   model   delta    sigma   weight residual
     111.36  113.62   -2.26 1.09e+00 8.42e-01 4.30e+00
  ... (remaining 3862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.03: 1455
       14.03 -    28.05: 134
       28.05 -    42.08: 33
       42.08 -    56.10: 4
       56.10 -    70.13: 1
  Dihedral angle restraints: 1627
    sinusoidal: 551
      harmonic: 1076
  Sorted by residual:
  dihedral pdb=" CG  ARG A 249 "
           pdb=" CD  ARG A 249 "
           pdb=" NE  ARG A 249 "
           pdb=" CZ  ARG A 249 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.43   43.57     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CB  MET A 119 "
           pdb=" CG  MET A 119 "
           pdb=" SD  MET A 119 "
           pdb=" CE  MET A 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  111.66  -51.66     3      1.50e+01 4.44e-03 9.04e+00
  dihedral pdb=" CA  LEU A 105 "
           pdb=" C   LEU A 105 "
           pdb=" N   VAL A 106 "
           pdb=" CA  VAL A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.97  -15.03     0      5.00e+00 4.00e-02 9.03e+00
  ... (remaining 1624 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 280
       0.032 -    0.063: 126
       0.063 -    0.095: 41
       0.095 -    0.126: 15
       0.126 -    0.158: 3
  Chirality restraints: 465
  Sorted by residual:
  chirality pdb=" CA  PHE A 127 "
            pdb=" N   PHE A 127 "
            pdb=" C   PHE A 127 "
            pdb=" CB  PHE A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.22e-01
  chirality pdb=" CA  ILE D  30 "
            pdb=" N   ILE D  30 "
            pdb=" C   ILE D  30 "
            pdb=" CB  ILE D  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CA  PRO A 309 "
            pdb=" N   PRO A 309 "
            pdb=" C   PRO A 309 "
            pdb=" CB  PRO A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 462 not shown)

  Planarity restraints: 470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  46 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" C   LEU A  46 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LEU A  46 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR A  47 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 211 "   -0.013 2.00e-02 2.50e+03   2.67e-02 7.10e+00
        pdb=" C   TYR A 211 "    0.046 2.00e-02 2.50e+03
        pdb=" O   TYR A 211 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 212 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 219 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO A 220 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 467 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1094
        2.90 -     3.40: 2578
        3.40 -     3.90: 4120
        3.90 -     4.40: 4429
        4.40 -     4.90: 8105
  Nonbonded interactions: 20326
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  43 "
            pdb=" OG1 THR A  47 "
     model   vdw
     2.404 3.040
  nonbonded pdb=" O   GLY A  57 "
            pdb=" ND2 ASN A  61 "
     model   vdw
     2.439 3.120
  nonbonded pdb=" O   VAL A 298 "
            pdb=" OG1 THR A 301 "
     model   vdw
     2.458 3.040
  nonbonded pdb=" OH  TYR A  71 "
            pdb=" OD1 ASN A 325 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" O   ASP D 111 "
            pdb=" OD1 ASP D 111 "
     model   vdw
     2.521 3.040
  ... (remaining 20321 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             1.920
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.010
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2837  Z= 0.182
  Angle     :  0.639   7.955   3871  Z= 0.363
  Chirality :  0.042   0.158    465
  Planarity :  0.006   0.050    470
  Dihedral  : 11.756  70.125    927
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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 are not related in a simple way.
  whole: -1.07 (0.41), residues: 355
  helix:  0.01 (0.31), residues: 225
  sheet: -0.48 (0.64), residues: 64
  loop : -3.07 (0.57), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 253 
 TYR   0.014   0.002   TYR A 228 
 PHE   0.013   0.001   PHE A 217 
 TRP   0.010   0.001   TRP D  38 
 HIS   0.003   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 2835)
  covalent geometry    : angle       0.63934 ( 3867)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.64136 (    4)
  hydrogen bonds       : bond        0.13484 (  198)
  hydrogen bonds       : angle       5.04257 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8448 (t) cc_final: 0.8085 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0443
  time to fit residues: 1.9104
Evaluate side-chains
  30 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0030
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0270
   overall best weight:    0.3848

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.140249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.112287 restraints weight = 3266.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.99
r_work: 0.3040 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   2837  Z= 0.135
  Angle     :  0.503   6.731   3871  Z= 0.278
  Chirality :  0.038   0.121    465
  Planarity :  0.005   0.039    470
  Dihedral  :  3.632  14.791    396
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.72 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.45), residues: 355
  helix:  1.82 (0.34), residues: 226
  sheet: -0.09 (0.66), residues: 64
  loop : -1.52 (0.74), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 253 
 TYR   0.011   0.001   TYR A 228 
 PHE   0.012   0.001   PHE A 213 
 TRP   0.004   0.001   TRP D  38 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 2835)
  covalent geometry    : angle       0.50286 ( 3867)
  SS BOND              : bond        0.00165 (    2)
  SS BOND              : angle       0.60936 (    4)
  hydrogen bonds       : bond        0.06479 (  198)
  hydrogen bonds       : angle       3.87736 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8066 (t) cc_final: 0.7612 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 30
  average time/residue: 0.0436
  time to fit residues: 1.7642
Evaluate side-chains
  29 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0470
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.141510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.113470 restraints weight = 3271.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.92
r_work: 0.3029 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2837  Z= 0.150
  Angle     :  0.506   5.497   3871  Z= 0.281
  Chirality :  0.039   0.129    465
  Planarity :  0.004   0.037    470
  Dihedral  :  3.560  14.364    396
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.09 %
    Favored  : 91.79 %
  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 are not related in a simple way.
  whole:  1.88 (0.46), residues: 355
  helix:  2.22 (0.34), residues: 224
  sheet:  0.23 (0.67), residues: 64
  loop : -1.10 (0.82), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 252 
 TYR   0.014   0.001   TYR A 211 
 PHE   0.014   0.001   PHE A 213 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.003   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2835)
  covalent geometry    : angle       0.50523 ( 3867)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       0.72076 (    4)
  hydrogen bonds       : bond        0.07138 (  198)
  hydrogen bonds       : angle       3.78657 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8269 (t) cc_final: 0.7814 (m)
  outliers start: 3
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0358
  time to fit residues: 1.6332
Evaluate side-chains
  36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  293 MET
Chi-restraints excluded: chain D residue  105 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.134489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.106058 restraints weight = 3241.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.91
r_work: 0.2968 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2837  Z= 0.170
  Angle     :  0.522   4.864   3871  Z= 0.291
  Chirality :  0.040   0.127    465
  Planarity :  0.005   0.035    470
  Dihedral  :  3.655  14.898    396
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.70 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.46), residues: 355
  helix:  2.15 (0.33), residues: 228
  sheet:  0.41 (0.68), residues: 64
  loop : -0.91 (0.88), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 252 
 TYR   0.015   0.001   TYR A 228 
 PHE   0.013   0.001   PHE A 213 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.003   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2835)
  covalent geometry    : angle       0.52179 ( 3867)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       0.84243 (    4)
  hydrogen bonds       : bond        0.07790 (  198)
  hydrogen bonds       : angle       3.80009 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8250 (t) cc_final: 0.7825 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0429
  time to fit residues: 1.9239
Evaluate side-chains
  35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  293 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.138423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.110266 restraints weight = 3252.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.91
r_work: 0.3012 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2837  Z= 0.145
  Angle     :  0.485   4.918   3871  Z= 0.271
  Chirality :  0.039   0.124    465
  Planarity :  0.004   0.035    470
  Dihedral  :  3.572  14.529    396
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.19 %
    Favored  : 87.69 %
  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 are not related in a simple way.
  whole:  2.20 (0.46), residues: 355
  helix:  2.34 (0.34), residues: 228
  sheet:  0.52 (0.68), residues: 64
  loop : -0.86 (0.87), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 252 
 TYR   0.013   0.001   TYR A 211 
 PHE   0.011   0.001   PHE A 213 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2835)
  covalent geometry    : angle       0.48502 ( 3867)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.74690 (    4)
  hydrogen bonds       : bond        0.06905 (  198)
  hydrogen bonds       : angle       3.68753 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8233 (t) cc_final: 0.7824 (m)
  outliers start: 3
  outliers final: 2
  residues processed: 33
  average time/residue: 0.0358
  time to fit residues: 1.6282
Evaluate side-chains
  32 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  217 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0980
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0570
   chunk 12 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3498

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.150672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123884 restraints weight = 3231.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.95
r_work: 0.3248 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2837  Z= 0.120
  Angle     :  0.447   4.957   3871  Z= 0.248
  Chirality :  0.037   0.117    465
  Planarity :  0.004   0.034    470
  Dihedral  :  3.412  14.002    396
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.45 %
    Favored  : 87.69 %
  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 are not related in a simple way.
  whole:  2.64 (0.47), residues: 355
  helix:  2.61 (0.34), residues: 227
  sheet:  0.69 (0.67), residues: 66
  loop : -0.37 (0.93), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 252 
 TYR   0.011   0.001   TYR A 211 
 PHE   0.008   0.001   PHE A 213 
 TRP   0.004   0.001   TRP D 106 
 HIS   0.001   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 2835)
  covalent geometry    : angle       0.44636 ( 3867)
  SS BOND              : bond        0.00125 (    2)
  SS BOND              : angle       0.61637 (    4)
  hydrogen bonds       : bond        0.05673 (  198)
  hydrogen bonds       : angle       3.54003 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  281 SER cc_start: 0.7919 (t) cc_final: 0.7560 (m)
  outliers start: 5
  outliers final: 3
  residues processed: 34
  average time/residue: 0.0316
  time to fit residues: 1.4647
Evaluate side-chains
  34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  299 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.145688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.118801 restraints weight = 3143.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.89
r_work: 0.3191 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2837  Z= 0.161
  Angle     :  0.502   4.894   3871  Z= 0.280
  Chirality :  0.039   0.122    465
  Planarity :  0.004   0.036    470
  Dihedral  :  3.523  14.673    396
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.82 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.46), residues: 355
  helix:  2.39 (0.34), residues: 228
  sheet:  0.76 (0.67), residues: 66
  loop : -0.51 (0.92), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 252 
 TYR   0.016   0.001   TYR A 228 
 PHE   0.012   0.001   PHE A 213 
 TRP   0.007   0.001   TRP D 106 
 HIS   0.003   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2835)
  covalent geometry    : angle       0.50149 ( 3867)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.84911 (    4)
  hydrogen bonds       : bond        0.07465 (  198)
  hydrogen bonds       : angle       3.68185 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.062 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 32
  average time/residue: 0.0395
  time to fit residues: 1.7332
Evaluate side-chains
  34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain D residue  105 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.139833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.112365 restraints weight = 3266.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.83
r_work: 0.3102 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2837  Z= 0.154
  Angle     :  0.491   4.971   3871  Z= 0.274
  Chirality :  0.039   0.121    465
  Planarity :  0.004   0.036    470
  Dihedral  :  3.545  14.335    396
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.31 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.46), residues: 355
  helix:  2.38 (0.34), residues: 228
  sheet:  0.82 (0.67), residues: 66
  loop : -0.48 (0.92), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 252 
 TYR   0.014   0.001   TYR A 228 
 PHE   0.010   0.001   PHE A 213 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.003   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 2835)
  covalent geometry    : angle       0.49044 ( 3867)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.79672 (    4)
  hydrogen bonds       : bond        0.07169 (  198)
  hydrogen bonds       : angle       3.67921 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8184 (t) cc_final: 0.7791 (m)
  outliers start: 4
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0300
  time to fit residues: 1.4199
Evaluate side-chains
  35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  299 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.133269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.104904 restraints weight = 3345.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.92
r_work: 0.2957 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2837  Z= 0.173
  Angle     :  0.523   4.981   3871  Z= 0.291
  Chirality :  0.040   0.126    465
  Planarity :  0.004   0.039    470
  Dihedral  :  3.633  14.540    396
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.31 %
    Favored  : 85.82 %
  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 are not related in a simple way.
  whole:  2.28 (0.46), residues: 355
  helix:  2.26 (0.34), residues: 228
  sheet:  0.84 (0.66), residues: 66
  loop : -0.57 (0.91), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 252 
 TYR   0.016   0.001   TYR A 228 
 PHE   0.013   0.001   PHE A 272 
 TRP   0.007   0.001   TRP D 106 
 HIS   0.003   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 2835)
  covalent geometry    : angle       0.52227 ( 3867)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.89707 (    4)
  hydrogen bonds       : bond        0.07948 (  198)
  hydrogen bonds       : angle       3.77632 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 32
  average time/residue: 0.0374
  time to fit residues: 1.6495
Evaluate side-chains
  34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain D residue  105 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0570
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.139509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.111991 restraints weight = 3308.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.85
r_work: 0.3062 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2837  Z= 0.128
  Angle     :  0.457   4.894   3871  Z= 0.255
  Chirality :  0.038   0.115    465
  Planarity :  0.004   0.036    470
  Dihedral  :  3.452  13.575    396
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.69 %
    Favored  : 85.82 %
  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 are not related in a simple way.
  whole:  2.67 (0.47), residues: 355
  helix:  2.53 (0.34), residues: 228
  sheet:  1.01 (0.67), residues: 66
  loop : -0.32 (0.93), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 252 
 TYR   0.012   0.001   TYR A 211 
 PHE   0.009   0.001   PHE A 213 
 TRP   0.004   0.001   TRP D  38 
 HIS   0.001   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2835)
  covalent geometry    : angle       0.45674 ( 3867)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.70534 (    4)
  hydrogen bonds       : bond        0.06095 (  198)
  hydrogen bonds       : angle       3.59034 (  576)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  281 SER cc_start: 0.8078 (t) cc_final: 0.7705 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0349
  time to fit residues: 1.6290
Evaluate side-chains
  34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  217 PHE
Chi-restraints excluded: chain A residue  299 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   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 = 0.3521 r_free = 0.3521 target = 0.138567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.111267 restraints weight = 3268.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.82
r_work: 0.2998 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2837  Z= 0.158
  Angle     :  0.500   4.975   3871  Z= 0.278
  Chirality :  0.039   0.121    465
  Planarity :  0.004   0.036    470
  Dihedral  :  3.549  14.057    396
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 13.06 %
    Favored  : 85.82 %
  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 are not related in a simple way.
  whole:  2.53 (0.47), residues: 355
  helix:  2.40 (0.34), residues: 228
  sheet:  1.01 (0.67), residues: 66
  loop : -0.42 (0.93), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 252 
 TYR   0.015   0.001   TYR A 228 
 PHE   0.012   0.001   PHE A 272 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.003   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2835)
  covalent geometry    : angle       0.49984 ( 3867)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.84210 (    4)
  hydrogen bonds       : bond        0.07293 (  198)
  hydrogen bonds       : angle       3.68527 (  576)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 905.55 seconds
wall clock time: 16 minutes 2.51 seconds (962.51 seconds total)