Starting phenix.real_space_refine
on Fri Oct 10 14:58:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ubz_42110/10_2025/8ubz_42110_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ubz_42110/10_2025/8ubz_42110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ubz_42110/10_2025/8ubz_42110_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ubz_42110/10_2025/8ubz_42110_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ubz_42110/10_2025/8ubz_42110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ubz_42110/10_2025/8ubz_42110.map"
  }
  resolution = 3.02
  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=   0.000 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2243      2.51       5
     N     496      2.21       5
     O     602      1.98       5
     H    3315      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6674
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 6536
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 17, 'TRANS': 397}
    Chain: "A"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 138
          Unusual residues: {'CHT': 1, 'Y01': 3}
          Classifications: {'undetermined': 4, 'water': 26}
          Link IDs: {None: 29}
  Time building chain proxies: 1.64, per 1000 atoms: 0.25
  Number of scatterers: 6674
  At special positions: 0
  Unit cell: (84.252, 56.994, 66.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     O     602      8.00
     N     496      7.00
     C    2243      6.00
     H    3315      1.00
    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: 0.58
  Conformation dependent library (CDL) restraints added in 281.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      90.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 131
      removed outlier: 3.886A  pdb=" N   VAL A 109 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ASN A 121 " --> pdb=" O   TYR A 117 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   TYR A 128 " --> pdb=" O   GLN A 124 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   SER A 129 " --> pdb=" O   TRP A 125 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ILE A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 140
    Processing helix  chain 'A' and resid 142 through 171
      removed outlier: 3.913A  pdb=" N   ILE A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
      removed outlier: 5.616A  pdb=" N   PHE A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 3.697A  pdb=" N   THR A 176 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A 193 " --> pdb=" O   TRP A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 219
      removed outlier: 3.712A  pdb=" N   THR A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   PHE A 216 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 4.367A  pdb=" N   ARG A 223 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 260
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 266 through 296
      removed outlier: 3.670A  pdb=" N   LEU A 270 " --> pdb=" O   ASP A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.859A  pdb=" N   ASN A 331 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 363
      removed outlier: 5.074A  pdb=" N   ASN A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   GLN A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   TYR A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 396
    Processing helix  chain 'A' and resid 399 through 420
    Processing helix  chain 'A' and resid 421 through 423
      No H-bonds generated for 'chain 'A' and resid 421 through 423'
    Processing helix  chain 'A' and resid 424 through 454
      removed outlier: 3.505A  pdb=" N   LEU A 443 " --> pdb=" O   MET A 439 " (cutoff:3.500A)
      Proline residue:  A 444  - end of helix
    Processing helix  chain 'A' and resid 458 through 489
    Processing helix  chain 'A' and resid 489 through 511
      removed outlier: 3.900A  pdb=" N   GLY A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    825 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: 1.45

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3307
        1.03 -     1.23: 11
        1.23 -     1.42: 1383
        1.42 -     1.61: 2010
        1.61 -     1.81: 28
  Bond restraints: 6739
  Sorted by residual:
  bond pdb=" CB  PRO A 231 "
       pdb=" CG  PRO A 231 "
    ideal  model  delta    sigma   weight residual
    1.492  1.558 -0.066 5.00e-02 4.00e+02 1.75e+00
  bond pdb=" CA  LEU A 220 "
       pdb=" C   LEU A 220 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 1.26e-02 6.30e+03 4.31e-01
  bond pdb=" CB  PRO A 257 "
       pdb=" CG  PRO A 257 "
    ideal  model  delta    sigma   weight residual
    1.492  1.523 -0.031 5.00e-02 4.00e+02 3.89e-01
  bond pdb=" CG  GLN A 197 "
       pdb=" CD  GLN A 197 "
    ideal  model  delta    sigma   weight residual
    1.516  1.531 -0.015 2.50e-02 1.60e+03 3.77e-01
  bond pdb=" C   LEU A 220 "
       pdb=" O   LEU A 220 "
    ideal  model  delta    sigma   weight residual
    1.244  1.238  0.006 9.80e-03 1.04e+04 3.42e-01
  ... (remaining 6734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 12036
        1.68 -     3.36: 119
        3.36 -     5.04: 13
        5.04 -     6.73: 2
        6.73 -     8.41: 1
  Bond angle restraints: 12171
  Sorted by residual:
  angle pdb=" C   GLY A 219 "
        pdb=" N   LEU A 220 "
        pdb=" CA  LEU A 220 "
      ideal   model   delta    sigma   weight residual
     120.09  123.77   -3.68 1.25e+00 6.40e-01 8.66e+00
  angle pdb=" CB  PRO A 159 "
        pdb=" CG  PRO A 159 "
        pdb=" CD  PRO A 159 "
      ideal   model   delta    sigma   weight residual
     106.10   97.69    8.41 3.20e+00 9.77e-02 6.90e+00
  angle pdb=" CA  PRO A 159 "
        pdb=" CB  PRO A 159 "
        pdb=" CG  PRO A 159 "
      ideal   model   delta    sigma   weight residual
     104.50   99.61    4.89 1.90e+00 2.77e-01 6.61e+00
  angle pdb=" CA  PRO A 159 "
        pdb=" N   PRO A 159 "
        pdb=" CD  PRO A 159 "
      ideal   model   delta    sigma   weight residual
     112.00  108.68    3.32 1.40e+00 5.10e-01 5.64e+00
  angle pdb=" N   PRO A 159 "
        pdb=" CA  PRO A 159 "
        pdb=" CB  PRO A 159 "
      ideal   model   delta    sigma   weight residual
     103.46  101.38    2.08 9.30e-01 1.16e+00 5.01e+00
  ... (remaining 12166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 2960
       17.40 -    34.80: 239
       34.80 -    52.20: 90
       52.20 -    69.60: 50
       69.60 -    87.00: 3
  Dihedral angle restraints: 3342
    sinusoidal: 1874
      harmonic: 1468
  Sorted by residual:
  dihedral pdb=" CA  TYR A 117 "
           pdb=" C   TYR A 117 "
           pdb=" N   SER A 118 "
           pdb=" CA  SER A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.53   17.47     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CB  MET A 413 "
           pdb=" CG  MET A 413 "
           pdb=" SD  MET A 413 "
           pdb=" CE  MET A 413 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.85  -59.15     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  LYS A 491 "
           pdb=" CG  LYS A 491 "
           pdb=" CD  LYS A 491 "
           pdb=" CE  LYS A 491 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.51  -57.49     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 3339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 426
       0.029 -    0.058: 68
       0.058 -    0.087: 58
       0.087 -    0.115: 11
       0.115 -    0.144: 1
  Chirality restraints: 564
  Sorted by residual:
  chirality pdb=" CA  PRO A 231 "
            pdb=" N   PRO A 231 "
            pdb=" C   PRO A 231 "
            pdb=" CB  PRO A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  PRO A 221 "
            pdb=" N   PRO A 221 "
            pdb=" C   PRO A 221 "
            pdb=" CB  PRO A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.61e-01
  chirality pdb=" CA  TYR A 117 "
            pdb=" N   TYR A 117 "
            pdb=" C   TYR A 117 "
            pdb=" CB  TYR A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.40e-01
  ... (remaining 561 not shown)

  Planarity restraints: 949
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 256 "    0.052 5.00e-02 4.00e+02   7.81e-02 9.77e+00
        pdb=" N   PRO A 257 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A 257 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 257 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 230 "   -0.051 5.00e-02 4.00e+02   7.57e-02 9.17e+00
        pdb=" N   PRO A 231 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 231 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 231 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 158 "    0.040 5.00e-02 4.00e+02   5.99e-02 5.74e+00
        pdb=" N   PRO A 159 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 159 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 159 "    0.033 5.00e-02 4.00e+02
  ... (remaining 946 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 815
        2.26 -     2.84: 15343
        2.84 -     3.43: 18619
        3.43 -     4.01: 24731
        4.01 -     4.60: 38275
  Nonbonded interactions: 97783
  Sorted by model distance:
  nonbonded pdb="HD22 ASN A 133 "
            pdb=" OE2 GLU A 367 "
     model   vdw
     1.669 2.450
  nonbonded pdb=" O   ALA A 450 "
            pdb=" HG1 THR A 454 "
     model   vdw
     1.728 2.450
  nonbonded pdb=" O   SER A 282 "
            pdb=" HG1 THR A 286 "
     model   vdw
     1.731 2.450
  nonbonded pdb=" O   ASN A 467 "
            pdb="HE21 GLN A 471 "
     model   vdw
     1.798 2.450
  nonbonded pdb=" O   LYS A 191 "
            pdb=" HG  SER A 194 "
     model   vdw
     1.840 2.450
  ... (remaining 97778 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:             4.880
  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:             0.050
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.430
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
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      :  0.002   0.066   3424  Z= 0.102
  Angle     :  0.482   8.408   4688  Z= 0.254
  Chirality :  0.033   0.144    564
  Planarity :  0.006   0.078    552
  Dihedral  : 15.414  87.005   1357
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 18.52 %
    Favored  : 81.20 %
  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:  3.77 (0.43), residues: 413
  helix:  3.14 (0.28), residues: 341
  sheet:  None (None), residues: 0
  loop : -1.00 (0.74), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 372 
 TYR   0.016   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 391 
 HIS   0.000   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3424)
  covalent geometry    : angle       0.48175 ( 4688)
  hydrogen bonds       : bond        0.11289 (  275)
  hydrogen bonds       : angle       5.56429 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 GLU cc_start: 0.8182 (tp30) cc_final: 0.7910 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1420
  time to fit residues: 15.7504
Evaluate side-chains
  54 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.120439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.103405 restraints weight = 17960.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.36
r_work: 0.3361 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3424  Z= 0.186
  Angle     :  0.550   5.749   4688  Z= 0.291
  Chirality :  0.036   0.137    564
  Planarity :  0.005   0.054    552
  Dihedral  :  5.346  53.281    658
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.52 %
    Favored  : 78.63 %
  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:  3.45 (0.40), residues: 413
  helix:  2.97 (0.27), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.71 (0.64), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 326 
 TYR   0.021   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A 496 
 TRP   0.008   0.001   TRP A 391 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3424)
  covalent geometry    : angle       0.54965 ( 4688)
  hydrogen bonds       : bond        0.04923 (  275)
  hydrogen bonds       : angle       4.25897 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7373 (ttp-170)
REVERT: A  298 GLU cc_start: 0.8670 (tp30) cc_final: 0.7912 (tt0)
REVERT: A  452 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7792 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 65
  average time/residue: 0.1260
  time to fit residues: 10.3805
Evaluate side-chains
  55 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  411 ILE
Chi-restraints excluded: chain A residue  469 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.117332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.100202 restraints weight = 18026.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.38
r_work: 0.3290 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3424  Z= 0.172
  Angle     :  0.519   4.835   4688  Z= 0.278
  Chirality :  0.036   0.132    564
  Planarity :  0.005   0.046    552
  Dihedral  :  5.186  42.353    658
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.80 %
    Favored  : 78.92 %
  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:  3.28 (0.41), residues: 413
  helix:  2.84 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.74 (0.62), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 106 
 TYR   0.021   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 391 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3424)
  covalent geometry    : angle       0.51891 ( 4688)
  hydrogen bonds       : bond        0.05022 (  275)
  hydrogen bonds       : angle       4.21835 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7413 (ttp-170)
REVERT: A  388 CYS cc_start: 0.8756 (m) cc_final: 0.8358 (m)
  outliers start: 8
  outliers final: 2
  residues processed: 63
  average time/residue: 0.1566
  time to fit residues: 12.1370
Evaluate side-chains
  53 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  361 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.115698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.098777 restraints weight = 18340.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.38
r_work: 0.3269 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3424  Z= 0.174
  Angle     :  0.526   5.327   4688  Z= 0.281
  Chirality :  0.036   0.167    564
  Planarity :  0.004   0.044    552
  Dihedral  :  5.247  41.661    658
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 20.23 %
    Favored  : 78.06 %
  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:  3.17 (0.41), residues: 413
  helix:  2.77 (0.27), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.77 (0.60), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.020   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3424)
  covalent geometry    : angle       0.52645 ( 4688)
  hydrogen bonds       : bond        0.05016 (  275)
  hydrogen bonds       : angle       4.14664 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  388 CYS cc_start: 0.8754 (m) cc_final: 0.8360 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1390
  time to fit residues: 10.5493
Evaluate side-chains
  58 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  166 TRP
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  469 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.098124 restraints weight = 18248.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.40
r_work: 0.3240 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3424  Z= 0.171
  Angle     :  0.521   5.254   4688  Z= 0.280
  Chirality :  0.036   0.142    564
  Planarity :  0.004   0.042    552
  Dihedral  :  5.231  41.474    658
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.80 %
    Favored  : 79.20 %
  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:  3.11 (0.41), residues: 413
  helix:  2.73 (0.27), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.78 (0.60), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A 416 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.001   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3424)
  covalent geometry    : angle       0.52089 ( 4688)
  hydrogen bonds       : bond        0.05005 (  275)
  hydrogen bonds       : angle       4.16243 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 CYS cc_start: 0.8724 (m) cc_final: 0.8303 (m)
  outliers start: 7
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1303
  time to fit residues: 10.0807
Evaluate side-chains
  59 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  166 TRP
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0870
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3615 r_free = 0.3615 target = 0.115929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.098528 restraints weight = 18019.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.40
r_work: 0.3252 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3424  Z= 0.140
  Angle     :  0.496   4.924   4688  Z= 0.266
  Chirality :  0.035   0.135    564
  Planarity :  0.004   0.042    552
  Dihedral  :  5.061  40.641    658
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 20.23 %
    Favored  : 78.35 %
  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:  3.21 (0.41), residues: 413
  helix:  2.79 (0.27), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.72 (0.62), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 301 
 TYR   0.019   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3424)
  covalent geometry    : angle       0.49570 ( 4688)
  hydrogen bonds       : bond        0.04758 (  275)
  hydrogen bonds       : angle       4.06683 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 CYS cc_start: 0.8721 (m) cc_final: 0.8307 (m)
  outliers start: 5
  outliers final: 5
  residues processed: 57
  average time/residue: 0.1388
  time to fit residues: 9.9819
Evaluate side-chains
  57 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  166 TRP
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.117233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.099508 restraints weight = 17863.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.44
r_work: 0.3270 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3424  Z= 0.118
  Angle     :  0.474   4.759   4688  Z= 0.253
  Chirality :  0.034   0.119    564
  Planarity :  0.004   0.041    552
  Dihedral  :  4.745  39.938    658
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.09 %
    Favored  : 78.63 %
  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:  3.37 (0.41), residues: 413
  helix:  2.92 (0.27), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.73 (0.63), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 423 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.009   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3424)
  covalent geometry    : angle       0.47421 ( 4688)
  hydrogen bonds       : bond        0.04401 (  275)
  hydrogen bonds       : angle       3.95672 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 CYS cc_start: 0.8727 (m) cc_final: 0.8318 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1552
  time to fit residues: 12.2082
Evaluate side-chains
  65 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  312 GLN
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    0.0000
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.4584

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.116904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.099452 restraints weight = 17999.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.43
r_work: 0.3265 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3424  Z= 0.128
  Angle     :  0.497   4.796   4688  Z= 0.266
  Chirality :  0.034   0.147    564
  Planarity :  0.004   0.041    552
  Dihedral  :  4.662  39.757    658
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.09 %
    Favored  : 78.63 %
  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:  3.38 (0.41), residues: 413
  helix:  2.91 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.77 (0.63), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 301 
 TYR   0.019   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3424)
  covalent geometry    : angle       0.49713 ( 4688)
  hydrogen bonds       : bond        0.04393 (  275)
  hydrogen bonds       : angle       3.95192 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 TYR cc_start: 0.7706 (m-80) cc_final: 0.7432 (m-80)
REVERT: A  388 CYS cc_start: 0.8711 (m) cc_final: 0.8293 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1714
  time to fit residues: 12.6382
Evaluate side-chains
  62 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  166 TRP
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.115856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.098657 restraints weight = 18269.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.45
r_work: 0.3255 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3424  Z= 0.147
  Angle     :  0.508   4.731   4688  Z= 0.270
  Chirality :  0.035   0.138    564
  Planarity :  0.005   0.040    552
  Dihedral  :  4.743  39.830    658
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.09 %
    Favored  : 78.63 %
  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:  3.25 (0.41), residues: 413
  helix:  2.83 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.81 (0.62), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 301 
 TYR   0.019   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A 496 
 TRP   0.005   0.001   TRP A 500 
 HIS   0.001   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3424)
  covalent geometry    : angle       0.50825 ( 4688)
  hydrogen bonds       : bond        0.04552 (  275)
  hydrogen bonds       : angle       3.98736 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 TYR cc_start: 0.7648 (m-80) cc_final: 0.7392 (m-80)
REVERT: A  388 CYS cc_start: 0.8720 (m) cc_final: 0.8277 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1367
  time to fit residues: 10.2048
Evaluate side-chains
  60 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.116950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.099582 restraints weight = 18082.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.44
r_work: 0.3268 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3424  Z= 0.126
  Angle     :  0.498   5.001   4688  Z= 0.266
  Chirality :  0.034   0.143    564
  Planarity :  0.004   0.040    552
  Dihedral  :  4.591  39.581    658
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.94 %
    Favored  : 78.06 %
  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:  3.30 (0.41), residues: 413
  helix:  2.86 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.77 (0.63), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 301 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3424)
  covalent geometry    : angle       0.49771 ( 4688)
  hydrogen bonds       : bond        0.04395 (  275)
  hydrogen bonds       : angle       4.01750 (  825)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7679 (ttm110)
REVERT: A  321 TYR cc_start: 0.7696 (m-80) cc_final: 0.7444 (m-80)
REVERT: A  388 CYS cc_start: 0.8692 (m) cc_final: 0.8270 (m)
  outliers start: 7
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1402
  time to fit residues: 10.4327
Evaluate side-chains
  60 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   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 = 0.3613 r_free = 0.3613 target = 0.116015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.099104 restraints weight = 18026.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.38
r_work: 0.3257 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3424  Z= 0.149
  Angle     :  0.519   6.632   4688  Z= 0.276
  Chirality :  0.035   0.158    564
  Planarity :  0.004   0.041    552
  Dihedral  :  4.693  39.714    658
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 20.23 %
    Favored  : 78.06 %
  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:  3.15 (0.41), residues: 413
  helix:  2.75 (0.27), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.80 (0.62), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 301 
 TYR   0.019   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A 496 
 TRP   0.005   0.001   TRP A 391 
 HIS   0.001   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3424)
  covalent geometry    : angle       0.51918 ( 4688)
  hydrogen bonds       : bond        0.04568 (  275)
  hydrogen bonds       : angle       4.07609 (  825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2137.12 seconds
wall clock time: 37 minutes 4.93 seconds (2224.93 seconds total)