Starting phenix.real_space_refine
on Fri Aug 22 13:21:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qcz_18338/08_2025/8qcz_18338.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qcz_18338/08_2025/8qcz_18338.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/8qcz_18338/08_2025/8qcz_18338.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qcz_18338/08_2025/8qcz_18338.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qcz_18338/08_2025/8qcz_18338.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qcz_18338/08_2025/8qcz_18338.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=   0.004 sd=   0.107
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      19      5.16       5
     C    2210      2.51       5
     N     524      2.21       5
     O     562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3316
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3273
          Classifications: {'peptide': 421}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 405}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.76, per 1000 atoms: 0.23
  Number of scatterers: 3316
  At special positions: 0
  Unit cell: (80.352, 58.59, 64.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      19     16.00
     O     562      8.00
     N     524      7.00
     C    2210      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 126.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      91.0% alpha, 0.0% 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 83 through 108
      removed outlier: 3.689A  pdb=" N   ILE A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   TYR A 105 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   GLY A 106 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE A 108 " --> pdb=" O   GLN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 4.150A  pdb=" N   HIS A 114 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 149
      removed outlier: 3.606A  pdb=" N   ILE A 123 " --> pdb=" O   SER A 119 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   TYR A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   MET A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE A 135 " --> pdb=" O   MET A 131 " (cutoff:3.500A)
      Proline residue:  A 136  - end of helix
      removed outlier: 5.115A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 149 through 170
      removed outlier: 3.506A  pdb=" N   ILE A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 169 " --> pdb=" O   ALA A 165 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY A 170 " --> pdb=" O   TRP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 4.261A  pdb=" N   THR A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A 192 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   PHE A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 206
    Processing helix  chain 'A' and resid 207 through 209
      No H-bonds generated for 'chain 'A' and resid 207 through 209'
    Processing helix  chain 'A' and resid 210 through 232
      removed outlier: 3.585A  pdb=" N   ILE A 226 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LEU A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
    Processing helix  chain 'A' and resid 242 through 272
      removed outlier: 3.551A  pdb=" N   MET A 253 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 290
      removed outlier: 3.714A  pdb=" N   ALA A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 307
    Processing helix  chain 'A' and resid 307 through 339
      removed outlier: 4.750A  pdb=" N   ASN A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   ARG A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS A 338 " --> pdb=" O   MET A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 372
      removed outlier: 4.033A  pdb=" N   VAL A 354 " --> pdb=" O   GLY A 350 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 357 " --> pdb=" O   ILE A 353 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 396
    Processing helix  chain 'A' and resid 400 through 431
      removed outlier: 3.591A  pdb=" N   VAL A 404 " --> pdb=" O   HIS A 400 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A 419 " --> pdb=" O   MET A 415 " (cutoff:3.500A)
      Proline residue:  A 420  - end of helix
    Processing helix  chain 'A' and resid 434 through 464
      removed outlier: 3.576A  pdb=" N   LEU A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 486
      removed outlier: 3.514A  pdb=" N   GLY A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU A 473 " --> pdb=" O   GLY A 469 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 498

    263 hydrogen bonds defined for protein.
    789 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: 0.45

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.38: 1319
        1.38 -     1.55: 2051
        1.55 -     1.72: 0
        1.72 -     1.89: 31
        1.89 -     2.06: 4
  Bond restraints: 3405
  Sorted by residual:
  bond pdb=" CG  HIS A 338 "
       pdb=" CD2 HIS A 338 "
    ideal  model  delta    sigma   weight residual
    1.354  1.325  0.029 1.10e-02 8.26e+03 7.02e+00
  bond pdb=" N   ARG A 348 "
       pdb=" CA  ARG A 348 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.73e+00
  bond pdb=" N   LEU A 132 "
       pdb=" CA  LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.032 1.33e-02 5.65e+03 5.72e+00
  bond pdb=" N   HIS A 338 "
       pdb=" CA  HIS A 338 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.28e-02 6.10e+03 4.86e+00
  bond pdb=" N   LYS A 375 "
       pdb=" CA  LYS A 375 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.026 1.26e-02 6.30e+03 4.42e+00
  ... (remaining 3400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 4502
        1.52 -     3.04: 111
        3.04 -     4.56: 26
        4.56 -     6.08: 9
        6.08 -     7.60: 3
  Bond angle restraints: 4651
  Sorted by residual:
  angle pdb=" C   ALA A 120 "
        pdb=" N   PHE A 121 "
        pdb=" CA  PHE A 121 "
      ideal   model   delta    sigma   weight residual
     120.29  115.19    5.10 1.42e+00 4.96e-01 1.29e+01
  angle pdb=" N   PHE A 121 "
        pdb=" CA  PHE A 121 "
        pdb=" C   PHE A 121 "
      ideal   model   delta    sigma   weight residual
     111.36  107.51    3.85 1.09e+00 8.42e-01 1.25e+01
  angle pdb=" N   HIS A 338 "
        pdb=" CA  HIS A 338 "
        pdb=" C   HIS A 338 "
      ideal   model   delta    sigma   weight residual
     113.88  109.85    4.03 1.23e+00 6.61e-01 1.08e+01
  angle pdb=" N   MET A 197 "
        pdb=" CA  MET A 197 "
        pdb=" C   MET A 197 "
      ideal   model   delta    sigma   weight residual
     109.81  117.01   -7.20 2.21e+00 2.05e-01 1.06e+01
  angle pdb=" CA  LEU A 139 "
        pdb=" C   LEU A 139 "
        pdb=" N   PRO A 140 "
      ideal   model   delta    sigma   weight residual
     120.77  123.84   -3.07 9.70e-01 1.06e+00 1.00e+01
  ... (remaining 4646 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 1694
       16.03 -    32.05: 170
       32.05 -    48.08: 57
       48.08 -    64.11: 12
       64.11 -    80.13: 5
  Dihedral angle restraints: 1938
    sinusoidal: 730
      harmonic: 1208
  Sorted by residual:
  dihedral pdb=" CA  TYR A  94 "
           pdb=" C   TYR A  94 "
           pdb=" N   SER A  95 "
           pdb=" CA  SER A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.52   19.48     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" C2D HEM A 601 "
           pdb=" C3D HEM A 601 "
           pdb=" CAD HEM A 601 "
           pdb=" CBD HEM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   78.36  -78.36     2      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" C1A HEM A 601 "
           pdb=" C2A HEM A 601 "
           pdb=" CAA HEM A 601 "
           pdb=" CBA HEM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  103.37   76.63     2      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 1935 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 367
       0.032 -    0.064: 133
       0.064 -    0.096: 30
       0.096 -    0.128: 9
       0.128 -    0.160: 3
  Chirality restraints: 542
  Sorted by residual:
  chirality pdb=" CA  ARG A 370 "
            pdb=" N   ARG A 370 "
            pdb=" C   ARG A 370 "
            pdb=" CB  ARG A 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  HIS A 338 "
            pdb=" N   HIS A 338 "
            pdb=" C   HIS A 338 "
            pdb=" CB  HIS A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  MET A 197 "
            pdb=" N   MET A 197 "
            pdb=" C   MET A 197 "
            pdb=" CB  MET A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 539 not shown)

  Planarity restraints: 559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 467 "    0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO A 468 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 468 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 468 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 337 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   TRP A 337 "    0.028 2.00e-02 2.50e+03
        pdb=" O   TRP A 337 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   HIS A 338 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 132 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   LEU A 132 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU A 132 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR A 133 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 556 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 827
        2.79 -     3.32: 3454
        3.32 -     3.84: 5559
        3.84 -     4.37: 6841
        4.37 -     4.90: 11678
  Nonbonded interactions: 28359
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 274 "
            pdb=" OE1 GLU A 274 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   LYS A 168 "
            pdb=" OG  SER A 171 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   TYR A 374 "
            pdb=" OG1 THR A 378 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   ALA A 283 "
            pdb=" OH  TYR A 431 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   THR A 373 "
            pdb=" OG1 THR A 373 "
     model   vdw
     2.327 3.040
  ... (remaining 28354 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.070
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
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   0.032   3405  Z= 0.189
  Angle     :  0.628   7.602   4651  Z= 0.349
  Chirality :  0.038   0.160    542
  Planarity :  0.004   0.050    559
  Dihedral  : 15.355  80.133   1168
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.62 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.21 (0.40), residues: 417
  helix:  0.39 (0.26), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.56 (0.83), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  82 
 TYR   0.017   0.001   TYR A 392 
 PHE   0.007   0.001   PHE A 413 
 TRP   0.013   0.001   TRP A 125 
 HIS   0.007   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3405)
  covalent geometry    : angle       0.62848 ( 4651)
  hydrogen bonds       : bond        0.22917 (  263)
  hydrogen bonds       : angle       8.29154 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A  194 ILE cc_start: 0.8108 (mm) cc_final: 0.7810 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0373
  time to fit residues: 2.9498
Evaluate side-chains
  55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.131376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.111079 restraints weight = 3924.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.30
r_work: 0.3126 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3405  Z= 0.158
  Angle     :  0.591   8.423   4651  Z= 0.299
  Chirality :  0.040   0.143    542
  Planarity :  0.004   0.038    559
  Dihedral  :  7.290  78.358    459
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.35 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.48 (0.40), residues: 417
  helix:  1.30 (0.26), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.62 (0.90), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.020   0.001   TYR A  94 
 PHE   0.013   0.001   PHE A 472 
 TRP   0.006   0.001   TRP A 205 
 HIS   0.002   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3405)
  covalent geometry    : angle       0.59122 ( 4651)
  hydrogen bonds       : bond        0.04618 (  263)
  hydrogen bonds       : angle       4.91413 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6836 (tt0)
REVERT: A  194 ILE cc_start: 0.8409 (mm) cc_final: 0.8112 (mt)
REVERT: A  216 SER cc_start: 0.8426 (m) cc_final: 0.8143 (p)
REVERT: A  456 SER cc_start: 0.8542 (t) cc_final: 0.8113 (p)
  outliers start: 9
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0384
  time to fit residues: 3.4757
Evaluate side-chains
  50 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  270 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.127785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.104811 restraints weight = 3904.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.51
r_work: 0.3105 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3405  Z= 0.144
  Angle     :  0.562   8.269   4651  Z= 0.278
  Chirality :  0.039   0.148    542
  Planarity :  0.004   0.036    559
  Dihedral  :  7.260  78.265    459
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.76 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.75 (0.40), residues: 417
  helix:  1.49 (0.26), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.58 (0.90), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.014   0.001   PHE A 472 
 TRP   0.005   0.001   TRP A 205 
 HIS   0.002   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3405)
  covalent geometry    : angle       0.56196 ( 4651)
  hydrogen bonds       : bond        0.04044 (  263)
  hydrogen bonds       : angle       4.48262 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6484 (tt0)
REVERT: A  216 SER cc_start: 0.8342 (m) cc_final: 0.8042 (p)
REVERT: A  272 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7876 (t80)
REVERT: A  456 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7840 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 60
  average time/residue: 0.0418
  time to fit residues: 3.3840
Evaluate side-chains
  51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.128200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.105445 restraints weight = 3818.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.43
r_work: 0.3067 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3405  Z= 0.139
  Angle     :  0.551   8.336   4651  Z= 0.275
  Chirality :  0.039   0.151    542
  Planarity :  0.004   0.034    559
  Dihedral  :  7.242  78.170    459
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.62 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.93 (0.40), residues: 417
  helix:  1.63 (0.26), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.75 (0.86), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.014   0.001   PHE A 413 
 TRP   0.004   0.001   TRP A 205 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3405)
  covalent geometry    : angle       0.55139 ( 4651)
  hydrogen bonds       : bond        0.03857 (  263)
  hydrogen bonds       : angle       4.31335 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6399 (tt0)
REVERT: A  216 SER cc_start: 0.8348 (m) cc_final: 0.8035 (p)
REVERT: A  272 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7795 (t80)
REVERT: A  495 LYS cc_start: 0.7167 (mttt) cc_final: 0.6549 (pttm)
  outliers start: 10
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0359
  time to fit residues: 2.9500
Evaluate side-chains
  56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.127673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.103978 restraints weight = 3791.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.51
r_work: 0.3064 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3405  Z= 0.139
  Angle     :  0.557   8.151   4651  Z= 0.274
  Chirality :  0.039   0.154    542
  Planarity :  0.004   0.034    559
  Dihedral  :  7.221  78.100    459
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.33 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.95 (0.40), residues: 417
  helix:  1.66 (0.26), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.82 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  84 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.014   0.001   PHE A 413 
 TRP   0.006   0.001   TRP A 205 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3405)
  covalent geometry    : angle       0.55681 ( 4651)
  hydrogen bonds       : bond        0.03767 (  263)
  hydrogen bonds       : angle       4.25461 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6432 (tt0)
REVERT: A  201 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7437 (mp)
REVERT: A  216 SER cc_start: 0.8331 (m) cc_final: 0.8017 (p)
REVERT: A  272 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7743 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0397
  time to fit residues: 3.0535
Evaluate side-chains
  58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.128658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.105337 restraints weight = 3806.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.48
r_work: 0.3094 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3405  Z= 0.143
  Angle     :  0.557   8.095   4651  Z= 0.276
  Chirality :  0.039   0.160    542
  Planarity :  0.004   0.034    559
  Dihedral  :  7.232  78.074    459
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.03 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.40), residues: 417
  helix:  1.75 (0.26), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.68 (0.84), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  84 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.015   0.001   PHE A 413 
 TRP   0.005   0.001   TRP A 205 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3405)
  covalent geometry    : angle       0.55675 ( 4651)
  hydrogen bonds       : bond        0.03733 (  263)
  hydrogen bonds       : angle       4.23455 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6479 (tt0)
REVERT: A  201 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7472 (mp)
REVERT: A  216 SER cc_start: 0.8377 (m) cc_final: 0.8058 (p)
REVERT: A  272 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7695 (t80)
REVERT: A  495 LYS cc_start: 0.7174 (mttt) cc_final: 0.6557 (pttm)
  outliers start: 10
  outliers final: 5
  residues processed: 62
  average time/residue: 0.0380
  time to fit residues: 3.2133
Evaluate side-chains
  55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  444 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.130336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.106826 restraints weight = 3822.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.51
r_work: 0.3144 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3405  Z= 0.129
  Angle     :  0.554   8.636   4651  Z= 0.274
  Chirality :  0.038   0.161    542
  Planarity :  0.004   0.035    559
  Dihedral  :  7.185  77.860    459
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.45 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.41), residues: 417
  helix:  1.79 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.51 (0.86), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  84 
 TYR   0.020   0.001   TYR A  94 
 PHE   0.015   0.001   PHE A 413 
 TRP   0.004   0.001   TRP A 205 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3405)
  covalent geometry    : angle       0.55437 ( 4651)
  hydrogen bonds       : bond        0.03601 (  263)
  hydrogen bonds       : angle       4.16935 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6483 (tt0)
REVERT: A  201 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7515 (mp)
REVERT: A  216 SER cc_start: 0.8388 (m) cc_final: 0.8045 (p)
REVERT: A  272 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7734 (t80)
REVERT: A  373 THR cc_start: 0.8342 (p) cc_final: 0.8141 (p)
REVERT: A  459 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7350 (mm-40)
REVERT: A  495 LYS cc_start: 0.7191 (mttt) cc_final: 0.6548 (pttm)
  outliers start: 9
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0378
  time to fit residues: 3.1977
Evaluate side-chains
  54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.133163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109853 restraints weight = 3854.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.50
r_work: 0.3043 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3405  Z= 0.146
  Angle     :  0.569   8.109   4651  Z= 0.282
  Chirality :  0.039   0.167    542
  Planarity :  0.004   0.035    559
  Dihedral  :  7.223  77.949    459
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.74 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.40), residues: 417
  helix:  1.74 (0.26), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.46 (0.86), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  84 
 TYR   0.022   0.001   TYR A  94 
 PHE   0.017   0.001   PHE A 413 
 TRP   0.006   0.001   TRP A 205 
 HIS   0.001   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3405)
  covalent geometry    : angle       0.56876 ( 4651)
  hydrogen bonds       : bond        0.03665 (  263)
  hydrogen bonds       : angle       4.19135 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6437 (tt0)
REVERT: A  201 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7449 (mp)
REVERT: A  216 SER cc_start: 0.8370 (m) cc_final: 0.8042 (p)
REVERT: A  272 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7735 (t80)
REVERT: A  373 THR cc_start: 0.8351 (p) cc_final: 0.8150 (p)
REVERT: A  459 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7312 (mm-40)
REVERT: A  495 LYS cc_start: 0.7174 (mttt) cc_final: 0.6531 (pttm)
  outliers start: 9
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0509
  time to fit residues: 3.4688
Evaluate side-chains
  54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.135954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112549 restraints weight = 3810.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.49
r_work: 0.3132 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3405  Z= 0.127
  Angle     :  0.555   8.012   4651  Z= 0.275
  Chirality :  0.038   0.165    542
  Planarity :  0.004   0.035    559
  Dihedral  :  7.163  77.626    459
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.02 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.41), residues: 417
  helix:  1.85 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.46 (0.86), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  84 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.015   0.001   PHE A 413 
 TRP   0.004   0.001   TRP A 205 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3405)
  covalent geometry    : angle       0.55473 ( 4651)
  hydrogen bonds       : bond        0.03503 (  263)
  hydrogen bonds       : angle       4.11111 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6506 (tt0)
REVERT: A  201 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7558 (mp)
REVERT: A  216 SER cc_start: 0.8424 (m) cc_final: 0.8095 (p)
REVERT: A  373 THR cc_start: 0.8397 (p) cc_final: 0.8191 (p)
REVERT: A  456 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (m)
REVERT: A  459 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7358 (mm-40)
REVERT: A  495 LYS cc_start: 0.7207 (mttt) cc_final: 0.6574 (pttm)
  outliers start: 10
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0312
  time to fit residues: 2.3152
Evaluate side-chains
  55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   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 = 0.3580 r_free = 0.3580 target = 0.135510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112450 restraints weight = 3796.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.47
r_work: 0.3101 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3405  Z= 0.131
  Angle     :  0.568  10.024   4651  Z= 0.278
  Chirality :  0.038   0.161    542
  Planarity :  0.004   0.035    559
  Dihedral  :  7.178  77.724    459
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.02 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.40), residues: 417
  helix:  1.81 (0.26), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.49 (0.85), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  84 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.016   0.001   PHE A 413 
 TRP   0.005   0.001   TRP A 205 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3405)
  covalent geometry    : angle       0.56781 ( 4651)
  hydrogen bonds       : bond        0.03529 (  263)
  hydrogen bonds       : angle       4.09793 (  789)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6466 (tt0)
REVERT: A  201 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7507 (mp)
REVERT: A  216 SER cc_start: 0.8412 (m) cc_final: 0.8073 (p)
REVERT: A  353 ILE cc_start: 0.7675 (tt) cc_final: 0.7418 (tt)
REVERT: A  373 THR cc_start: 0.8395 (p) cc_final: 0.8193 (p)
REVERT: A  456 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.8061 (m)
REVERT: A  459 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7337 (mm-40)
REVERT: A  495 LYS cc_start: 0.7197 (mttt) cc_final: 0.6558 (pttm)
  outliers start: 9
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0374
  time to fit residues: 2.7657
Evaluate side-chains
  57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  456 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 6 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.135785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.112555 restraints weight = 3798.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.49
r_work: 0.3128 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3405  Z= 0.132
  Angle     :  0.577   9.679   4651  Z= 0.285
  Chirality :  0.038   0.161    542
  Planarity :  0.004   0.035    559
  Dihedral  :  7.176  77.762    459
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.59 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.40), residues: 417
  helix:  1.82 (0.26), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.49 (0.84), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  84 
 TYR   0.021   0.001   TYR A  94 
 PHE   0.016   0.001   PHE A 413 
 TRP   0.005   0.001   TRP A 205 
 HIS   0.001   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3405)
  covalent geometry    : angle       0.57705 ( 4651)
  hydrogen bonds       : bond        0.03507 (  263)
  hydrogen bonds       : angle       4.12500 (  789)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 683.36 seconds
wall clock time: 12 minutes 20.70 seconds (740.70 seconds total)