Starting phenix.real_space_refine
on Wed Sep 17 04:03:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m9y_63744/09_2025/9m9y_63744_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m9y_63744/09_2025/9m9y_63744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m9y_63744/09_2025/9m9y_63744_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m9y_63744/09_2025/9m9y_63744_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m9y_63744/09_2025/9m9y_63744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m9y_63744/09_2025/9m9y_63744.map"
  }
  resolution = 3.04
  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=   0.111
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      29      5.16       5
     C    2404      2.51       5
     N     613      2.21       5
     O     622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3668
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3668
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 24, 'TRANS': 450}
          Chain breaks: 4
  Time building chain proxies: 1.04, per 1000 atoms: 0.28
  Number of scatterers: 3668
  At special positions: 0
  Unit cell: (95.996, 59.648, 78.288, 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      29     16.00
     O     622      8.00
     N     613      7.00
     C    2404      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 136 " distance=2.04

  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: 0.32
  Conformation dependent library (CDL) restraints added in 146.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  876

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 1 sheets defined
      82.7% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 14 through 36
      removed outlier: 4.075A  pdb=" N   THR A  18 " --> pdb=" O   GLY A  14 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      Proline residue:  A  27  - end of helix
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 37 through 40
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 68 through 74
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 140 through 165
      removed outlier: 4.216A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 187
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 192 through 221
      removed outlier: 3.544A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 252
      removed outlier: 4.366A  pdb=" N   ALA A 228 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
    Processing helix  chain 'A' and resid 264 through 272
      removed outlier: 4.178A  pdb=" N   ALA A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 287
    Processing helix  chain 'A' and resid 288 through 303
    Processing helix  chain 'A' and resid 314 through 321
    Processing helix  chain 'A' and resid 339 through 365
      removed outlier: 3.508A  pdb=" N   ALA A 348 " --> pdb=" O   TRP A 344 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLY A 362 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 373 through 399
      removed outlier: 3.511A  pdb=" N   LEU A 377 " --> pdb=" O   ASP A 373 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 422
      removed outlier: 3.683A  pdb=" N   GLN A 405 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 456
      removed outlier: 3.635A  pdb=" N   PHE A 456 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 478
      removed outlier: 4.383A  pdb=" N   MET A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   THR A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.674A  pdb=" N   ILE A 482 " --> pdb=" O   MET A 478 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 478 through 483'
    Processing helix  chain 'A' and resid 484 through 487
      removed outlier: 3.872A  pdb=" N   GLN A 487 " --> pdb=" O   MET A 484 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 484 through 487'
    Processing helix  chain 'A' and resid 491 through 512
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88

    263 hydrogen bonds defined for protein.
    780 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: 0.57

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 552
        1.32 -     1.44: 1026
        1.44 -     1.56: 2132
        1.56 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 3755
  Sorted by residual:
  bond pdb=" C   ILE A  74 "
       pdb=" N   PRO A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.386 -0.057 1.18e-02 7.18e+03 2.29e+01
  bond pdb=" C   ILE A 404 "
       pdb=" O   ILE A 404 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.13e-02 7.83e+03 1.48e+01
  bond pdb=" C   LEU A 414 "
       pdb=" O   LEU A 414 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.17e-02 7.31e+03 1.38e+01
  bond pdb=" C   LEU A 377 "
       pdb=" O   LEU A 377 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.042 1.17e-02 7.31e+03 1.31e+01
  bond pdb=" C   THR A 392 "
       pdb=" O   THR A 392 "
    ideal  model  delta    sigma   weight residual
    1.236  1.195  0.041 1.18e-02 7.18e+03 1.21e+01
  ... (remaining 3750 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 4688
        2.16 -     4.33: 327
        4.33 -     6.49: 60
        6.49 -     8.65: 16
        8.65 -    10.81: 11
  Bond angle restraints: 5102
  Sorted by residual:
  angle pdb=" N   GLY A  12 "
        pdb=" CA  GLY A  12 "
        pdb=" C   GLY A  12 "
      ideal   model   delta    sigma   weight residual
     114.16  104.83    9.33 1.21e+00 6.83e-01 5.94e+01
  angle pdb=" C   LEU A 492 "
        pdb=" N   PRO A 493 "
        pdb=" CA  PRO A 493 "
      ideal   model   delta    sigma   weight residual
     120.38  112.67    7.71 1.03e+00 9.43e-01 5.61e+01
  angle pdb=" N   ASN A  39 "
        pdb=" CA  ASN A  39 "
        pdb=" C   ASN A  39 "
      ideal   model   delta    sigma   weight residual
     113.23  104.41    8.82 1.24e+00 6.50e-01 5.06e+01
  angle pdb=" N   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" C   PRO A  75 "
      ideal   model   delta    sigma   weight residual
     110.70  118.92   -8.22 1.22e+00 6.72e-01 4.54e+01
  angle pdb=" N   TRP A  93 "
        pdb=" CA  TRP A  93 "
        pdb=" C   TRP A  93 "
      ideal   model   delta    sigma   weight residual
     113.15  106.09    7.06 1.19e+00 7.06e-01 3.52e+01
  ... (remaining 5097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.75: 2010
       14.75 -    29.51: 168
       29.51 -    44.26: 28
       44.26 -    59.02: 5
       59.02 -    73.77: 1
  Dihedral angle restraints: 2212
    sinusoidal: 859
      harmonic: 1353
  Sorted by residual:
  dihedral pdb=" C   ARG A 401 "
           pdb=" N   ARG A 401 "
           pdb=" CA  ARG A 401 "
           pdb=" CB  ARG A 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.04   14.44     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" CB  CYS A  85 "
           pdb=" SG  CYS A  85 "
           pdb=" SG  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.52   43.52     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" N   ARG A 401 "
           pdb=" C   ARG A 401 "
           pdb=" CA  ARG A 401 "
           pdb=" CB  ARG A 401 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.96  -10.16     0      2.50e+00 1.60e-01 1.65e+01
  ... (remaining 2209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 491
       0.109 -    0.217: 93
       0.217 -    0.325: 11
       0.325 -    0.434: 4
       0.434 -    0.542: 1
  Chirality restraints: 600
  Sorted by residual:
  chirality pdb=" CA  ARG A 401 "
            pdb=" N   ARG A 401 "
            pdb=" C   ARG A 401 "
            pdb=" CB  ARG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.35e+00
  chirality pdb=" CA  TYR A 165 "
            pdb=" N   TYR A 165 "
            pdb=" C   TYR A 165 "
            pdb=" CB  TYR A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  TYR A 361 "
            pdb=" N   TYR A 361 "
            pdb=" C   TYR A 361 "
            pdb=" CB  TYR A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.00e+00
  ... (remaining 597 not shown)

  Planarity restraints: 627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  94 "   -0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   GLN A  94 "    0.068 2.00e-02 2.50e+03
        pdb=" O   GLN A  94 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   LEU A  95 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 344 "    0.017 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   TRP A 344 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   TRP A 344 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG A 345 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 152 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.42e+00
        pdb=" C   GLY A 152 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A 152 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A 153 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 624 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1487
        2.89 -     3.39: 3792
        3.39 -     3.89: 6313
        3.89 -     4.40: 7497
        4.40 -     4.90: 11679
  Nonbonded interactions: 30768
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  34 "
            pdb=" O   ALA A 262 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   GLU A 107 "
            pdb=" OG1 THR A 110 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   LEU A 396 "
            pdb=" O   LEU A 399 "
     model   vdw
     2.498 3.040
  nonbonded pdb=" N   GLY A  12 "
            pdb=" N   VAL A  13 "
     model   vdw
     2.503 2.560
  nonbonded pdb=" N   TRP A  93 "
            pdb=" N   GLN A  94 "
     model   vdw
     2.513 2.560
  ... (remaining 30763 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:             0.640
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.420
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
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      :  0.009   0.057   3757  Z= 0.700
  Angle     :  1.353  10.813   5106  Z= 0.903
  Chirality :  0.089   0.542    600
  Planarity :  0.008   0.057    627
  Dihedral  : 10.656  73.771   1330
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.40), residues: 465
  helix:  0.81 (0.29), residues: 349
  sheet: -3.79 (1.08), residues: 10
  loop : -1.18 (0.59), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 473 
 TYR   0.021   0.003   TYR A 165 
 PHE   0.023   0.002   PHE A 211 
 TRP   0.015   0.002   TRP A 255 
 HIS   0.007   0.002   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00932 ( 3755)
  covalent geometry    : angle       1.35109 ( 5102)
  SS BOND              : bond        0.00444 (    2)
  SS BOND              : angle       3.15806 (    4)
  hydrogen bonds       : bond        0.20104 (  263)
  hydrogen bonds       : angle       7.25044 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  317 MET cc_start: 0.4709 (mmm) cc_final: 0.3828 (ptp)
REVERT: A  411 MET cc_start: 0.7711 (tpt) cc_final: 0.7477 (tpt)
REVERT: A  426 LEU cc_start: 0.8085 (mt) cc_final: 0.7867 (mt)
REVERT: A  477 MET cc_start: 0.8468 (ttm) cc_final: 0.8252 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0951
  time to fit residues: 5.6794
Evaluate side-chains
  38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A  80 GLN
A  83 HIS
A 242 GLN
A 405 GLN
A 487 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.176728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125682 restraints weight = 3677.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.46
r_work: 0.3390 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3757  Z= 0.165
  Angle     :  0.590   6.645   5106  Z= 0.300
  Chirality :  0.040   0.147    600
  Planarity :  0.006   0.044    627
  Dihedral  :  3.844  15.506    502
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.81 %
    Favored  : 93.69 %
  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 aren not related in a simple way.
  whole:  1.85 (0.40), residues: 465
  helix:  1.80 (0.28), residues: 350
  sheet: -4.20 (0.97), residues: 10
  loop : -0.02 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 121 
 TYR   0.018   0.002   TYR A 165 
 PHE   0.016   0.002   PHE A 211 
 TRP   0.011   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3755)
  covalent geometry    : angle       0.58893 ( 5102)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       1.17885 (    4)
  hydrogen bonds       : bond        0.04770 (  263)
  hydrogen bonds       : angle       4.34178 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   53 MET cc_start: 0.7725 (mtp) cc_final: 0.7519 (mtp)
REVERT: A  317 MET cc_start: 0.4896 (mmm) cc_final: 0.3924 (ptp)
REVERT: A  349 MET cc_start: 0.8007 (tpp) cc_final: 0.7760 (tpp)
REVERT: A  411 MET cc_start: 0.7725 (tpt) cc_final: 0.7476 (tpt)
REVERT: A  477 MET cc_start: 0.8141 (ttm) cc_final: 0.7848 (ttm)
  outliers start: 2
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0687
  time to fit residues: 4.3221
Evaluate side-chains
  42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0370
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.177317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.123226 restraints weight = 3726.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.56
r_work: 0.3344 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3757  Z= 0.135
  Angle     :  0.522   6.686   5106  Z= 0.260
  Chirality :  0.038   0.149    600
  Planarity :  0.005   0.043    627
  Dihedral  :  3.642  15.890    502
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.58 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.41), residues: 465
  helix:  2.21 (0.28), residues: 352
  sheet: -4.36 (0.88), residues: 10
  loop :  0.13 (0.70), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 121 
 TYR   0.016   0.002   TYR A 165 
 PHE   0.011   0.001   PHE A 211 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3755)
  covalent geometry    : angle       0.52139 ( 5102)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       0.83490 (    4)
  hydrogen bonds       : bond        0.04091 (  263)
  hydrogen bonds       : angle       3.94317 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  317 MET cc_start: 0.5117 (mmm) cc_final: 0.4104 (ptp)
REVERT: A  411 MET cc_start: 0.7715 (tpt) cc_final: 0.7448 (tpt)
  outliers start: 4
  outliers final: 3
  residues processed: 50
  average time/residue: 0.0570
  time to fit residues: 3.7202
Evaluate side-chains
  45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 29 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.176110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.122684 restraints weight = 3710.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.55
r_work: 0.3338 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3757  Z= 0.129
  Angle     :  0.521   6.696   5106  Z= 0.251
  Chirality :  0.037   0.147    600
  Planarity :  0.004   0.038    627
  Dihedral  :  3.577  15.947    502
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  9.85 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.41), residues: 465
  helix:  2.29 (0.28), residues: 354
  sheet: -4.39 (0.85), residues: 10
  loop :  0.46 (0.72), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 121 
 TYR   0.014   0.002   TYR A 165 
 PHE   0.012   0.001   PHE A 511 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3755)
  covalent geometry    : angle       0.52062 ( 5102)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       0.73466 (    4)
  hydrogen bonds       : bond        0.03809 (  263)
  hydrogen bonds       : angle       3.82608 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  317 MET cc_start: 0.5331 (mmm) cc_final: 0.4307 (ptp)
REVERT: A  411 MET cc_start: 0.7721 (tpt) cc_final: 0.7441 (tpt)
  outliers start: 4
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0548
  time to fit residues: 3.5863
Evaluate side-chains
  50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.0970
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.171321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.117660 restraints weight = 3749.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.55
r_work: 0.3309 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3757  Z= 0.203
  Angle     :  0.579   6.807   5106  Z= 0.284
  Chirality :  0.040   0.146    600
  Planarity :  0.004   0.036    627
  Dihedral  :  3.743  15.322    502
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.85 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.41), residues: 465
  helix:  2.10 (0.28), residues: 353
  sheet: -4.75 (0.77), residues: 10
  loop :  0.56 (0.72), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.014   0.002   TYR A 165 
 PHE   0.013   0.002   PHE A 266 
 TRP   0.010   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 3755)
  covalent geometry    : angle       0.57841 ( 5102)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       0.81953 (    4)
  hydrogen bonds       : bond        0.04422 (  263)
  hydrogen bonds       : angle       4.00044 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  211 PHE cc_start: 0.6247 (m-10) cc_final: 0.5546 (m-80)
REVERT: A  301 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6674 (mtm180)
REVERT: A  385 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7346 (m-30)
REVERT: A  411 MET cc_start: 0.7800 (tpt) cc_final: 0.7578 (tpt)
  outliers start: 8
  outliers final: 7
  residues processed: 47
  average time/residue: 0.0567
  time to fit residues: 3.4964
Evaluate side-chains
  50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 41 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.172853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.122872 restraints weight = 3721.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.43
r_work: 0.3349 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3757  Z= 0.110
  Angle     :  0.502   6.720   5106  Z= 0.242
  Chirality :  0.037   0.145    600
  Planarity :  0.004   0.036    627
  Dihedral  :  3.528  15.513    502
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.36 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.41), residues: 465
  helix:  2.34 (0.28), residues: 354
  sheet: -4.80 (0.73), residues: 10
  loop :  0.79 (0.73), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.012   0.001   TYR A 165 
 PHE   0.013   0.001   PHE A 511 
 TRP   0.010   0.001   TRP A 255 
 HIS   0.002   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3755)
  covalent geometry    : angle       0.50235 ( 5102)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.65449 (    4)
  hydrogen bonds       : bond        0.03624 (  263)
  hydrogen bonds       : angle       3.77183 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  301 ARG cc_start: 0.6985 (mtm180) cc_final: 0.6722 (mtm180)
REVERT: A  411 MET cc_start: 0.7705 (tpt) cc_final: 0.7370 (tpt)
  outliers start: 8
  outliers final: 6
  residues processed: 50
  average time/residue: 0.0508
  time to fit residues: 3.4195
Evaluate side-chains
  50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0060
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.174780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.121777 restraints weight = 3837.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.56
r_work: 0.3356 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3757  Z= 0.117
  Angle     :  0.502   6.854   5106  Z= 0.242
  Chirality :  0.037   0.144    600
  Planarity :  0.004   0.035    627
  Dihedral  :  3.454  15.269    502
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.62 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.85 (0.41), residues: 465
  helix:  2.40 (0.28), residues: 354
  sheet: -4.71 (0.73), residues: 10
  loop :  0.86 (0.74), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.012   0.001   TYR A 165 
 PHE   0.008   0.001   PHE A 205 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3755)
  covalent geometry    : angle       0.50153 ( 5102)
  SS BOND              : bond        0.00244 (    2)
  SS BOND              : angle       0.64930 (    4)
  hydrogen bonds       : bond        0.03579 (  263)
  hydrogen bonds       : angle       3.76961 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   35 MET cc_start: 0.8599 (ttp) cc_final: 0.8388 (ttm)
REVERT: A  301 ARG cc_start: 0.7038 (mtm180) cc_final: 0.6753 (mtm180)
REVERT: A  411 MET cc_start: 0.7721 (tpt) cc_final: 0.7402 (tpt)
  outliers start: 8
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0568
  time to fit residues: 3.7829
Evaluate side-chains
  53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 3 optimal weight:    0.2980
   chunk 24 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.173528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.120673 restraints weight = 3847.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.55
r_work: 0.3340 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3757  Z= 0.131
  Angle     :  0.518   6.916   5106  Z= 0.248
  Chirality :  0.037   0.142    600
  Planarity :  0.004   0.035    627
  Dihedral  :  3.504  14.763    502
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.12 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.41), residues: 465
  helix:  2.34 (0.28), residues: 355
  sheet: -4.70 (0.70), residues: 10
  loop :  0.99 (0.75), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.012   0.002   TYR A 165 
 PHE   0.009   0.001   PHE A 205 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3755)
  covalent geometry    : angle       0.51772 ( 5102)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       0.63391 (    4)
  hydrogen bonds       : bond        0.03691 (  263)
  hydrogen bonds       : angle       3.79875 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  301 ARG cc_start: 0.7065 (mtm180) cc_final: 0.6411 (mtm180)
REVERT: A  411 MET cc_start: 0.7769 (tpt) cc_final: 0.7438 (tpt)
REVERT: A  444 SER cc_start: 0.8818 (t) cc_final: 0.8520 (t)
  outliers start: 6
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0548
  time to fit residues: 3.5949
Evaluate side-chains
  52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0270
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.171739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.122814 restraints weight = 3751.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.39
r_work: 0.3359 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3757  Z= 0.125
  Angle     :  0.509   6.886   5106  Z= 0.245
  Chirality :  0.037   0.142    600
  Planarity :  0.004   0.036    627
  Dihedral  :  3.466  14.703    502
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.37 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.41), residues: 465
  helix:  2.35 (0.28), residues: 355
  sheet: -4.61 (0.69), residues: 10
  loop :  1.09 (0.76), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.012   0.002   TYR A 165 
 PHE   0.009   0.001   PHE A 205 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3755)
  covalent geometry    : angle       0.50896 ( 5102)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.61615 (    4)
  hydrogen bonds       : bond        0.03615 (  263)
  hydrogen bonds       : angle       3.79494 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  301 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6633 (mtm180)
REVERT: A  411 MET cc_start: 0.7785 (tpt) cc_final: 0.7453 (tpt)
REVERT: A  444 SER cc_start: 0.8839 (t) cc_final: 0.8544 (t)
REVERT: A  512 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.5645 (tt)
  outliers start: 6
  outliers final: 5
  residues processed: 51
  average time/residue: 0.0524
  time to fit residues: 3.5815
Evaluate side-chains
  53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.171424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.122424 restraints weight = 3823.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.40
r_work: 0.3339 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3757  Z= 0.121
  Angle     :  0.509   6.776   5106  Z= 0.245
  Chirality :  0.037   0.142    600
  Planarity :  0.004   0.036    627
  Dihedral  :  3.484  14.669    502
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.63 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.85 (0.41), residues: 465
  helix:  2.35 (0.28), residues: 355
  sheet: -4.56 (0.70), residues: 10
  loop :  1.07 (0.75), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.011   0.001   TYR A 165 
 PHE   0.014   0.001   PHE A  24 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3755)
  covalent geometry    : angle       0.50933 ( 5102)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       0.60545 (    4)
  hydrogen bonds       : bond        0.03575 (  263)
  hydrogen bonds       : angle       3.80323 (  780)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  301 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6644 (mtm180)
REVERT: A  411 MET cc_start: 0.7800 (tpt) cc_final: 0.7471 (tpt)
REVERT: A  444 SER cc_start: 0.8853 (t) cc_final: 0.8549 (t)
REVERT: A  512 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.5632 (tt)
  outliers start: 6
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0556
  time to fit residues: 3.8833
Evaluate side-chains
  56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  512 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    0.0370
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 2 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.175027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.122079 restraints weight = 3742.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.52
r_work: 0.3334 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3757  Z= 0.115
  Angle     :  0.521   7.886   5106  Z= 0.246
  Chirality :  0.037   0.141    600
  Planarity :  0.004   0.036    627
  Dihedral  :  3.453  14.637    502
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.13 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.41), residues: 465
  helix:  2.37 (0.28), residues: 355
  sheet: -4.50 (0.73), residues: 10
  loop :  1.09 (0.75), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.011   0.001   TYR A 165 
 PHE   0.016   0.001   PHE A  24 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3755)
  covalent geometry    : angle       0.52086 ( 5102)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.59580 (    4)
  hydrogen bonds       : bond        0.03526 (  263)
  hydrogen bonds       : angle       3.80575 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 991.93 seconds
wall clock time: 17 minutes 39.11 seconds (1059.11 seconds total)