Starting phenix.real_space_refine
on Wed Sep 17 03:25:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9joz_61690/09_2025/9joz_61690.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9joz_61690/09_2025/9joz_61690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9joz_61690/09_2025/9joz_61690.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9joz_61690/09_2025/9joz_61690.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9joz_61690/09_2025/9joz_61690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9joz_61690/09_2025/9joz_61690.map"
  }
  resolution = 2.94
  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=   0.118
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      10      5.16       5
     C    2104      2.51       5
     N     515      2.21       5
     O     514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 3143
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3143
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 12, 'TRANS': 377}
          Chain breaks: 2
  Time building chain proxies: 1.08, per 1000 atoms: 0.34
  Number of scatterers: 3143
  At special positions: 0
  Unit cell: (68, 65, 75, 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      10     16.00
     O     514      8.00
     N     515      7.00
     C    2104      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: 0.28
  Conformation dependent library (CDL) restraints added in 124.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  738

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      85.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 40
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 68
      removed outlier: 3.569A  pdb=" N   ILE A  68 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 88
      removed outlier: 3.696A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   LEU A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   ALA A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 3.861A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
      removed outlier: 4.280A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.508A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
      removed outlier: 4.391A  pdb=" N   PHE A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 147
      No H-bonds generated for 'chain 'A' and resid 145 through 147'
    Processing helix  chain 'A' and resid 148 through 176
    Processing helix  chain 'A' and resid 181 through 201
    Processing helix  chain 'A' and resid 250 through 263
    Processing helix  chain 'A' and resid 264 through 294
      removed outlier: 3.512A  pdb=" N   TRP A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A 278 " --> pdb=" O   TRP A 274 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 325
      removed outlier: 3.671A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 355
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 390
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 395 through 419
    Processing helix  chain 'A' and resid 427 through 456

    240 hydrogen bonds defined for protein.
    720 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: 0.52

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 929
        1.34 -     1.46: 799
        1.46 -     1.58: 1487
        1.58 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3231
  Sorted by residual:
  bond pdb=" N   VAL A 288 "
       pdb=" CA  VAL A 288 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.30e-02 5.92e+03 1.03e+01
  bond pdb=" N   LYS A 393 "
       pdb=" CA  LYS A 393 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.23e-02 6.61e+03 6.60e+00
  bond pdb=" CA  SER A 138 "
       pdb=" CB  SER A 138 "
    ideal  model  delta    sigma   weight residual
    1.532  1.494  0.039 1.53e-02 4.27e+03 6.48e+00
  bond pdb=" N   SER A  73 "
       pdb=" CA  SER A  73 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.80e+00
  bond pdb=" N   SER A  75 "
       pdb=" CA  SER A  75 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.32e-02 5.74e+03 5.74e+00
  ... (remaining 3226 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 4217
        1.07 -     2.13: 122
        2.13 -     3.20: 49
        3.20 -     4.27: 5
        4.27 -     5.33: 6
  Bond angle restraints: 4399
  Sorted by residual:
  angle pdb=" N   SER A 138 "
        pdb=" CA  SER A 138 "
        pdb=" C   SER A 138 "
      ideal   model   delta    sigma   weight residual
     113.41  109.79    3.62 1.22e+00 6.72e-01 8.82e+00
  angle pdb=" C   PHE A 385 "
        pdb=" CA  PHE A 385 "
        pdb=" CB  PHE A 385 "
      ideal   model   delta    sigma   weight residual
     110.85  115.51   -4.66 1.70e+00 3.46e-01 7.50e+00
  angle pdb=" CA  PHE A 385 "
        pdb=" CB  PHE A 385 "
        pdb=" CG  PHE A 385 "
      ideal   model   delta    sigma   weight residual
     113.80  116.43   -2.63 1.00e+00 1.00e+00 6.93e+00
  angle pdb=" CA  LYS A 393 "
        pdb=" C   LYS A 393 "
        pdb=" O   LYS A 393 "
      ideal   model   delta    sigma   weight residual
     120.89  118.02    2.87 1.10e+00 8.26e-01 6.80e+00
  angle pdb=" O   SER A 313 "
        pdb=" C   SER A 313 "
        pdb=" N   THR A 314 "
      ideal   model   delta    sigma   weight residual
     122.07  124.68   -2.61 1.03e+00 9.43e-01 6.42e+00
  ... (remaining 4394 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 1598
       17.01 -    34.02: 187
       34.02 -    51.03: 45
       51.03 -    68.05: 15
       68.05 -    85.06: 5
  Dihedral angle restraints: 1850
    sinusoidal: 702
      harmonic: 1148
  Sorted by residual:
  dihedral pdb=" CA  LEU A 143 "
           pdb=" C   LEU A 143 "
           pdb=" N   VAL A 144 "
           pdb=" CA  VAL A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.50  -17.50     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.42  -16.58     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CB  GLU A  45 "
           pdb=" CG  GLU A  45 "
           pdb=" CD  GLU A  45 "
           pdb=" OE1 GLU A  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.06  -85.06     1      3.00e+01 1.11e-03 9.75e+00
  ... (remaining 1847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 408
       0.047 -    0.094: 90
       0.094 -    0.141: 11
       0.141 -    0.188: 3
       0.188 -    0.235: 1
  Chirality restraints: 513
  Sorted by residual:
  chirality pdb=" CB  VAL A 144 "
            pdb=" CA  VAL A 144 "
            pdb=" CG1 VAL A 144 "
            pdb=" CG2 VAL A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.99e-01
  chirality pdb=" CB  ILE A 140 "
            pdb=" CA  ILE A 140 "
            pdb=" CG1 ILE A 140 "
            pdb=" CG2 ILE A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 510 not shown)

  Planarity restraints: 526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 303 "   -0.262 9.50e-02 1.11e+02   1.17e-01 8.45e+00
        pdb=" NE  ARG A 303 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 303 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 303 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO A  70 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 145 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO A 146 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 523 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 985
        2.82 -     3.34: 3149
        3.34 -     3.86: 5608
        3.86 -     4.38: 6478
        4.38 -     4.90: 10914
  Nonbonded interactions: 27134
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 339 "
            pdb=" OG1 THR A 343 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG  SER A 321 "
            pdb=" O   GLN A 377 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   LEU A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OH  TYR A  31 "
            pdb=" O   LEU A 199 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   TYR A 126 "
            pdb=" OG1 THR A 129 "
     model   vdw
     2.342 3.040
  ... (remaining 27129 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.460
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
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      :  0.003   0.042   3231  Z= 0.199
  Angle     :  0.514   5.334   4399  Z= 0.312
  Chirality :  0.040   0.235    513
  Planarity :  0.007   0.117    526
  Dihedral  : 16.758  85.057   1112
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 23.81 %
    Favored  : 75.30 %
  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:  1.34 (0.43), residues: 384
  helix:  1.57 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.53 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 330 
 TYR   0.010   0.001   TYR A 438 
 PHE   0.013   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3231)
  covalent geometry    : angle       0.51410 ( 4399)
  hydrogen bonds       : bond        0.10672 (  240)
  hydrogen bonds       : angle       4.91020 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.123 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 34
  average time/residue: 0.5277
  time to fit residues: 18.5633
Evaluate side-chains
  31 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   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 = 0.3664 r_free = 0.3664 target = 0.150865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.113827 restraints weight = 3363.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.06
r_work: 0.2998 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3231  Z= 0.162
  Angle     :  0.489   5.498   4399  Z= 0.261
  Chirality :  0.039   0.159    513
  Planarity :  0.005   0.058    526
  Dihedral  :  5.399  59.460    439
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.62 %
    Favored  : 74.11 %
  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:  1.76 (0.43), residues: 384
  helix:  1.83 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.21 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 330 
 TYR   0.014   0.001   TYR A  35 
 PHE   0.021   0.002   PHE A  84 
 TRP   0.014   0.002   TRP A 107 
 HIS   0.003   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3231)
  covalent geometry    : angle       0.48894 ( 4399)
  hydrogen bonds       : bond        0.04402 (  240)
  hydrogen bonds       : angle       3.90004 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 29
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   30 CYS cc_start: 0.8924 (m) cc_final: 0.8689 (m)
  outliers start: 11
  outliers final: 4
  residues processed: 37
  average time/residue: 0.5055
  time to fit residues: 19.3731
Evaluate side-chains
  32 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 30 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.152087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.115798 restraints weight = 3328.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.04
r_work: 0.3048 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3231  Z= 0.144
  Angle     :  0.475   5.386   4399  Z= 0.250
  Chirality :  0.038   0.163    513
  Planarity :  0.005   0.058    526
  Dihedral  :  4.746  58.304    437
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.81 %
    Favored  : 74.11 %
  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:  1.88 (0.44), residues: 384
  helix:  1.91 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -2.18 (0.73), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 330 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.020   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.005   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3231)
  covalent geometry    : angle       0.47455 ( 4399)
  hydrogen bonds       : bond        0.04161 (  240)
  hydrogen bonds       : angle       3.78725 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  262 LEU cc_start: 0.7506 (tp) cc_final: 0.7127 (mm)
  outliers start: 7
  outliers final: 5
  residues processed: 34
  average time/residue: 0.5194
  time to fit residues: 18.2968
Evaluate side-chains
  33 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 358 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.147895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.111160 restraints weight = 3291.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.99
r_work: 0.3007 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3231  Z= 0.149
  Angle     :  0.479   5.449   4399  Z= 0.253
  Chirality :  0.038   0.125    513
  Planarity :  0.005   0.056    526
  Dihedral  :  4.705  56.449    437
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.21 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.44), residues: 384
  helix:  1.95 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.31 (0.73), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 330 
 TYR   0.013   0.001   TYR A  35 
 PHE   0.021   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.004   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3231)
  covalent geometry    : angle       0.47884 ( 4399)
  hydrogen bonds       : bond        0.04141 (  240)
  hydrogen bonds       : angle       3.77656 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   25 TRP cc_start: 0.6200 (p90) cc_final: 0.5916 (p90)
REVERT: A   59 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7583 (m-10)
REVERT: A  263 ARG cc_start: 0.7693 (tpt90) cc_final: 0.7153 (tpp-160)
REVERT: A  456 ARG cc_start: 0.7429 (ptp-110) cc_final: 0.6514 (ttp80)
  outliers start: 10
  outliers final: 5
  residues processed: 37
  average time/residue: 0.6043
  time to fit residues: 23.0620
Evaluate side-chains
  35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.149673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.112945 restraints weight = 3302.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.04
r_work: 0.2982 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3231  Z= 0.158
  Angle     :  0.487   5.469   4399  Z= 0.256
  Chirality :  0.038   0.124    513
  Planarity :  0.005   0.056    526
  Dihedral  :  4.673  54.364    437
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.62 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.44), residues: 384
  helix:  1.96 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -2.29 (0.71), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 330 
 TYR   0.013   0.001   TYR A  35 
 PHE   0.022   0.002   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.004   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3231)
  covalent geometry    : angle       0.48655 ( 4399)
  hydrogen bonds       : bond        0.04225 (  240)
  hydrogen bonds       : angle       3.78937 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   59 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7590 (m-10)
REVERT: A  263 ARG cc_start: 0.7734 (tpt90) cc_final: 0.7261 (tpp-160)
REVERT: A  456 ARG cc_start: 0.7218 (ptp-110) cc_final: 0.6507 (ttp80)
  outliers start: 12
  outliers final: 7
  residues processed: 39
  average time/residue: 0.5705
  time to fit residues: 22.9429
Evaluate side-chains
  38 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.0980
   chunk 31 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0010
   overall best weight:    0.3386

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.151701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.115063 restraints weight = 3255.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.02
r_work: 0.3032 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3231  Z= 0.119
  Angle     :  0.453   5.427   4399  Z= 0.239
  Chirality :  0.037   0.124    513
  Planarity :  0.004   0.056    526
  Dihedral  :  4.544  53.302    437
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.92 %
    Favored  : 73.51 %
  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:  2.02 (0.44), residues: 384
  helix:  2.04 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -2.40 (0.71), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 330 
 TYR   0.011   0.001   TYR A 139 
 PHE   0.017   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3231)
  covalent geometry    : angle       0.45322 ( 4399)
  hydrogen bonds       : bond        0.03810 (  240)
  hydrogen bonds       : angle       3.64404 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  262 LEU cc_start: 0.7295 (tp) cc_final: 0.7056 (mm)
REVERT: A  456 ARG cc_start: 0.7114 (ptp-110) cc_final: 0.6460 (ttp80)
  outliers start: 12
  outliers final: 7
  residues processed: 37
  average time/residue: 0.5372
  time to fit residues: 20.5576
Evaluate side-chains
  35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   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 = 0.3604 r_free = 0.3604 target = 0.146736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.109600 restraints weight = 3398.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.03
r_work: 0.2993 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3231  Z= 0.159
  Angle     :  0.486   5.515   4399  Z= 0.256
  Chirality :  0.039   0.125    513
  Planarity :  0.005   0.055    526
  Dihedral  :  4.583  51.407    437
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.21 %
    Favored  : 73.51 %
  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:  1.92 (0.44), residues: 384
  helix:  1.97 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.31 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 330 
 TYR   0.014   0.001   TYR A  35 
 PHE   0.022   0.002   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3231)
  covalent geometry    : angle       0.48566 ( 4399)
  hydrogen bonds       : bond        0.04206 (  240)
  hydrogen bonds       : angle       3.75505 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.5317 (ptm160) cc_final: 0.4929 (ptm160)
REVERT: A  263 ARG cc_start: 0.7763 (tpt90) cc_final: 0.7292 (tpp-160)
REVERT: A  456 ARG cc_start: 0.7133 (ptp-110) cc_final: 0.6488 (ttp80)
  outliers start: 11
  outliers final: 6
  residues processed: 38
  average time/residue: 0.5885
  time to fit residues: 23.1015
Evaluate side-chains
  34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0170
   chunk 19 optimal weight:    0.3980
   chunk 17 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.2980
   chunk 31 optimal weight:    0.3980
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.3018

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

Flipped N/Q/H residues before XYZ refinement:
A 457 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.156121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120124 restraints weight = 3334.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.01
r_work: 0.3041 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3231  Z= 0.114
  Angle     :  0.451   5.455   4399  Z= 0.238
  Chirality :  0.037   0.127    513
  Planarity :  0.004   0.056    526
  Dihedral  :  4.463  50.747    437
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.70 %
    Favored  : 72.32 %
  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:  2.07 (0.44), residues: 384
  helix:  2.11 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.51 (0.70), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 330 
 TYR   0.011   0.001   TYR A 139 
 PHE   0.016   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3231)
  covalent geometry    : angle       0.45059 ( 4399)
  hydrogen bonds       : bond        0.03764 (  240)
  hydrogen bonds       : angle       3.61801 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.5274 (ptm160) cc_final: 0.4811 (ptm160)
REVERT: A  262 LEU cc_start: 0.7294 (tp) cc_final: 0.7042 (mm)
REVERT: A  456 ARG cc_start: 0.7056 (ptp-110) cc_final: 0.6384 (ttp80)
REVERT: A  457 HIS cc_start: 0.5792 (OUTLIER) cc_final: 0.5415 (p90)
  outliers start: 10
  outliers final: 7
  residues processed: 33
  average time/residue: 0.5547
  time to fit residues: 18.9593
Evaluate side-chains
  34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  457 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    0.0970
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.148717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.111553 restraints weight = 3356.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.05
r_work: 0.3033 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3231  Z= 0.143
  Angle     :  0.475   5.497   4399  Z= 0.251
  Chirality :  0.039   0.185    513
  Planarity :  0.005   0.056    526
  Dihedral  :  4.484  49.926    437
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 25.30 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.44), residues: 384
  helix:  2.04 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -2.47 (0.71), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 330 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.020   0.001   PHE A  84 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3231)
  covalent geometry    : angle       0.47514 ( 4399)
  hydrogen bonds       : bond        0.03982 (  240)
  hydrogen bonds       : angle       3.67221 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.5134 (ptm160) cc_final: 0.4642 (ptm160)
REVERT: A  262 LEU cc_start: 0.7296 (tp) cc_final: 0.7033 (mm)
REVERT: A  263 ARG cc_start: 0.7641 (tpt90) cc_final: 0.7080 (ttm-80)
REVERT: A  456 ARG cc_start: 0.7133 (ptp-110) cc_final: 0.6478 (ttp80)
  outliers start: 9
  outliers final: 6
  residues processed: 34
  average time/residue: 0.5901
  time to fit residues: 20.7031
Evaluate side-chains
  34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 457 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.148451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111206 restraints weight = 3268.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.05
r_work: 0.2991 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3231  Z= 0.154
  Angle     :  0.490   5.518   4399  Z= 0.258
  Chirality :  0.039   0.168    513
  Planarity :  0.005   0.056    526
  Dihedral  :  4.526  49.066    437
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.40 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.43), residues: 384
  helix:  2.02 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.38 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 330 
 TYR   0.013   0.001   TYR A  35 
 PHE   0.022   0.001   PHE A  84 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.007   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3231)
  covalent geometry    : angle       0.49016 ( 4399)
  hydrogen bonds       : bond        0.04147 (  240)
  hydrogen bonds       : angle       3.73056 (  720)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  262 LEU cc_start: 0.7319 (tp) cc_final: 0.7049 (mm)
REVERT: A  263 ARG cc_start: 0.7610 (tpt90) cc_final: 0.7046 (ttm-80)
REVERT: A  456 ARG cc_start: 0.7074 (ptp-110) cc_final: 0.6446 (ttp80)
  outliers start: 9
  outliers final: 6
  residues processed: 36
  average time/residue: 0.4915
  time to fit residues: 18.4122
Evaluate side-chains
  33 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 0 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 = 0.3623 r_free = 0.3623 target = 0.147555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.110445 restraints weight = 3347.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.05
r_work: 0.2975 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3231  Z= 0.171
  Angle     :  0.508   5.739   4399  Z= 0.266
  Chirality :  0.040   0.162    513
  Planarity :  0.005   0.055    526
  Dihedral  :  4.576  48.972    437
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 25.00 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.43), residues: 384
  helix:  1.95 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.37 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 145 
 TYR   0.015   0.001   TYR A  35 
 PHE   0.024   0.002   PHE A  84 
 TRP   0.013   0.002   TRP A 331 
 HIS   0.002   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 3231)
  covalent geometry    : angle       0.50846 ( 4399)
  hydrogen bonds       : bond        0.04297 (  240)
  hydrogen bonds       : angle       3.79709 (  720)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1297.80 seconds
wall clock time: 22 minutes 59.09 seconds (1379.09 seconds total)