Starting phenix.real_space_refine
on Fri Aug 22 14:06:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sdz_40355/08_2025/8sdz_40355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sdz_40355/08_2025/8sdz_40355.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sdz_40355/08_2025/8sdz_40355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sdz_40355/08_2025/8sdz_40355.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sdz_40355/08_2025/8sdz_40355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sdz_40355/08_2025/8sdz_40355.map"
  }
  resolution = 2.86
  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=   0.002
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      31      5.16       5
     C    2533      2.51       5
     N     654      2.21       5
     O     695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3913
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3872
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 26, 'TRANS': 473}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 41
          Unusual residues: {'RTO': 1}
          Classifications: {'undetermined': 1, 'water': 22}
          Link IDs: {None: 22}
  Time building chain proxies: 1.17, per 1000 atoms: 0.30
  Number of scatterers: 3913
  At special positions: 0
  Unit cell: (78.85, 71.38, 98.77, 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      31     16.00
     O     695      8.00
     N     654      7.00
     C    2533      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 128 " distance=2.02

  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: 0.36
  Conformation dependent library (CDL) restraints added in 202.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  928

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 2 sheets defined
      80.4% alpha, 1.2% 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 2 through 10
    Processing helix  chain 'A' and resid 14 through 26
    Processing helix  chain 'A' and resid 27 through 36
      removed outlier: 3.963A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   SER A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 62 through 66
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 127 through 130
    Processing helix  chain 'A' and resid 131 through 160
      removed outlier: 4.115A  pdb=" N   GLN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASP A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 158 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 181
    Processing helix  chain 'A' and resid 184 through 213
      removed outlier: 3.569A  pdb=" N   SER A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TRP A 213 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
      removed outlier: 6.057A  pdb=" N   HIS A 217 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 214 through 217'
    Processing helix  chain 'A' and resid 218 through 244
      removed outlier: 3.585A  pdb=" N   VAL A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 254
    Processing helix  chain 'A' and resid 256 through 265
      removed outlier: 3.711A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 268
      No H-bonds generated for 'chain 'A' and resid 266 through 268'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 296
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 305 through 314
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 332 through 355
      removed outlier: 3.580A  pdb=" N   HIS A 337 " --> pdb=" O   PRO A 333 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 377
    Processing helix  chain 'A' and resid 377 through 392
    Processing helix  chain 'A' and resid 393 through 415
    Processing helix  chain 'A' and resid 419 through 449
    Processing helix  chain 'A' and resid 453 through 477
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 502
      Proline residue:  A 494  - end of helix
      removed outlier: 3.880A  pdb=" N   ALA A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 524
      removed outlier: 3.834A  pdb=" N   LEU A 519 " --> pdb=" O   THR A 515 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81

    272 hydrogen bonds defined for protein.
    801 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: 0.64

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1217
        1.35 -     1.46: 974
        1.46 -     1.58: 1743
        1.58 -     1.70: 0
        1.70 -     1.82: 49
  Bond restraints: 3983
  Sorted by residual:
  bond pdb=" N04 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.625  1.712 -0.087 2.00e-02 2.50e+03 1.88e+01
  bond pdb=" C11 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.776  1.820 -0.044 2.00e-02 2.50e+03 4.78e+00
  bond pdb=" CB  PRO A 505 "
       pdb=" CG  PRO A 505 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.32e+00
  bond pdb=" CB  MET A  23 "
       pdb=" CG  MET A  23 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.28e-01
  bond pdb=" O09 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.446  1.462 -0.016 2.00e-02 2.50e+03 6.14e-01
  ... (remaining 3978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.62: 5394
        3.62 -     7.23: 23
        7.23 -    10.85: 1
       10.85 -    14.46: 0
       14.46 -    18.08: 1
  Bond angle restraints: 5419
  Sorted by residual:
  angle pdb=" O09 RTO A 601 "
        pdb=" S08 RTO A 601 "
        pdb=" O10 RTO A 601 "
      ideal   model   delta    sigma   weight residual
     119.19  101.11   18.08 3.00e+00 1.11e-01 3.63e+01
  angle pdb=" CB  MET A  23 "
        pdb=" CG  MET A  23 "
        pdb=" SD  MET A  23 "
      ideal   model   delta    sigma   weight residual
     112.70  122.34   -9.64 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" CA  MET A  23 "
        pdb=" CB  MET A  23 "
        pdb=" CG  MET A  23 "
      ideal   model   delta    sigma   weight residual
     114.10  119.50   -5.40 2.00e+00 2.50e-01 7.29e+00
  angle pdb=" CA  TYR A 264 "
        pdb=" CB  TYR A 264 "
        pdb=" CG  TYR A 264 "
      ideal   model   delta    sigma   weight residual
     113.90  118.00   -4.10 1.80e+00 3.09e-01 5.20e+00
  angle pdb=" N   VAL A 256 "
        pdb=" CA  VAL A 256 "
        pdb=" C   VAL A 256 "
      ideal   model   delta    sigma   weight residual
     108.88  113.75   -4.87 2.16e+00 2.14e-01 5.09e+00
  ... (remaining 5414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 2037
       16.88 -    33.76: 237
       33.76 -    50.64: 70
       50.64 -    67.52: 18
       67.52 -    84.40: 7
  Dihedral angle restraints: 2369
    sinusoidal: 926
      harmonic: 1443
  Sorted by residual:
  dihedral pdb=" CA  CYS A  49 "
           pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    2.02  -75.02     1      2.00e+01 2.50e-03 1.78e+01
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -113.39   27.39     1      1.00e+01 1.00e-02 1.08e+01
  dihedral pdb=" SG  CYS A  49 "
           pdb=" CB  CYS A 105 "
           pdb=" SG  CYS A 105 "
           pdb=" CA  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   24.03   54.97     1      2.00e+01 2.50e-03 1.02e+01
  ... (remaining 2366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 487
       0.039 -    0.077: 116
       0.077 -    0.116: 22
       0.116 -    0.154: 4
       0.154 -    0.193: 2
  Chirality restraints: 631
  Sorted by residual:
  chirality pdb=" CG  LEU A   6 "
            pdb=" CB  LEU A   6 "
            pdb=" CD1 LEU A   6 "
            pdb=" CD2 LEU A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.28e-01
  chirality pdb=" CG  LEU A 232 "
            pdb=" CB  LEU A 232 "
            pdb=" CD1 LEU A 232 "
            pdb=" CD2 LEU A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  ILE A  44 "
            pdb=" N   ILE A  44 "
            pdb=" C   ILE A  44 "
            pdb=" CB  ILE A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 628 not shown)

  Planarity restraints: 673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 213 "    0.014 2.00e-02 2.50e+03   1.38e-02 4.79e+00
        pdb=" CG  TRP A 213 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 213 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 213 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 213 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 213 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 213 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 213 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 213 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 213 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  26 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO A  27 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 256 "   -0.017 5.00e-02 4.00e+02   2.52e-02 1.02e+00
        pdb=" N   PRO A 257 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 257 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 257 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 670 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 67
        2.69 -     3.24: 3898
        3.24 -     3.79: 6341
        3.79 -     4.35: 8704
        4.35 -     4.90: 14135
  Nonbonded interactions: 33145
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 475 "
            pdb=" OG1 THR A 478 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER A  33 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OD1 ASN A 168 "
            pdb=" OG  SER A 201 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   LEU A  29 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   GLY A 233 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.234 3.040
  ... (remaining 33140 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.910
  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:6.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
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   0.087   3985  Z= 0.130
  Angle     :  0.588  18.076   5423  Z= 0.261
  Chirality :  0.036   0.193    631
  Planarity :  0.003   0.028    673
  Dihedral  : 16.554  84.396   1435
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.24 %
    Favored  : 78.33 %
  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:  0.91 (0.37), residues: 492
  helix:  0.73 (0.26), residues: 374
  sheet:  0.04 (1.43), residues: 10
  loop :  0.67 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 336 
 TYR   0.013   0.001   TYR A 264 
 PHE   0.007   0.001   PHE A 191 
 TRP   0.035   0.002   TRP A 213 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3983)
  covalent geometry    : angle       0.58831 ( 5419)
  SS BOND              : bond        0.00518 (    2)
  SS BOND              : angle       0.80018 (    4)
  hydrogen bonds       : bond        0.23340 (  272)
  hydrogen bonds       : angle       7.31566 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  280 ARG cc_start: 0.5134 (mmm160) cc_final: 0.4856 (tpp-160)
  outliers start: 6
  outliers final: 5
  residues processed: 65
  average time/residue: 0.5454
  time to fit residues: 36.6805
Evaluate side-chains
  60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  515 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 234 GLN
A 246 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.171557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130619 restraints weight = 4409.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.05
r_work: 0.3340 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3985  Z= 0.159
  Angle     :  0.572   6.801   5423  Z= 0.286
  Chirality :  0.039   0.160    631
  Planarity :  0.004   0.029    673
  Dihedral  :  7.099  66.507    571
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 18.33 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.38), residues: 492
  helix:  1.45 (0.27), residues: 368
  sheet:  0.53 (1.38), residues: 10
  loop :  1.00 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.024   0.001   TYR A 264 
 PHE   0.018   0.001   PHE A 351 
 TRP   0.018   0.002   TRP A 213 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3983)
  covalent geometry    : angle       0.57147 ( 5419)
  SS BOND              : bond        0.00937 (    2)
  SS BOND              : angle       0.72237 (    4)
  hydrogen bonds       : bond        0.05581 (  272)
  hydrogen bonds       : angle       4.80842 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 ASN cc_start: 0.7465 (m-40) cc_final: 0.6750 (t0)
REVERT: A  219 ARG cc_start: 0.4719 (ttt-90) cc_final: 0.4328 (mtt90)
REVERT: A  260 ILE cc_start: 0.7847 (mm) cc_final: 0.7622 (mt)
REVERT: A  327 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5620 (mmm)
  outliers start: 16
  outliers final: 6
  residues processed: 69
  average time/residue: 0.5157
  time to fit residues: 36.9071
Evaluate side-chains
  64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.173579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.132812 restraints weight = 4354.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.04
r_work: 0.3342 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3985  Z= 0.123
  Angle     :  0.493   6.171   5423  Z= 0.249
  Chirality :  0.037   0.129    631
  Planarity :  0.004   0.026    673
  Dihedral  :  6.682  63.785    566
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 18.81 %
    Favored  : 77.38 %
  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 (0.39), residues: 492
  helix:  1.55 (0.27), residues: 369
  sheet:  0.61 (1.32), residues: 10
  loop :  1.00 (0.65), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.017   0.001   PHE A 351 
 TRP   0.020   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3983)
  covalent geometry    : angle       0.49295 ( 5419)
  SS BOND              : bond        0.00629 (    2)
  SS BOND              : angle       0.71596 (    4)
  hydrogen bonds       : bond        0.04558 (  272)
  hydrogen bonds       : angle       4.37712 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 ASN cc_start: 0.7427 (m-40) cc_final: 0.6762 (t0)
REVERT: A   23 MET cc_start: 0.7488 (mmp) cc_final: 0.7175 (mmp)
REVERT: A  447 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8069 (mt-10)
  outliers start: 16
  outliers final: 8
  residues processed: 68
  average time/residue: 0.4613
  time to fit residues: 32.6849
Evaluate side-chains
  64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.173729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.132310 restraints weight = 4337.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.08
r_work: 0.3367 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3985  Z= 0.116
  Angle     :  0.475   6.319   5423  Z= 0.238
  Chirality :  0.037   0.124    631
  Planarity :  0.003   0.025    673
  Dihedral  :  6.592  61.414    566
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 18.57 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.39), residues: 492
  helix:  1.68 (0.27), residues: 368
  sheet:  0.50 (1.35), residues: 10
  loop :  0.93 (0.64), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.014   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.020   0.002   TRP A 213 
 HIS   0.002   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3983)
  covalent geometry    : angle       0.47511 ( 5419)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       0.68671 (    4)
  hydrogen bonds       : bond        0.04199 (  272)
  hydrogen bonds       : angle       4.17661 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 ASN cc_start: 0.7457 (m-40) cc_final: 0.6773 (t0)
REVERT: A   23 MET cc_start: 0.7481 (mmp) cc_final: 0.7173 (mmp)
REVERT: A  386 PHE cc_start: 0.6974 (m-10) cc_final: 0.6226 (t80)
REVERT: A  431 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7680 (tmtm)
  outliers start: 15
  outliers final: 9
  residues processed: 70
  average time/residue: 0.4146
  time to fit residues: 30.4225
Evaluate side-chains
  65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.173639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132809 restraints weight = 4313.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.05
r_work: 0.3344 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3985  Z= 0.116
  Angle     :  0.472   5.209   5423  Z= 0.237
  Chirality :  0.037   0.133    631
  Planarity :  0.003   0.025    673
  Dihedral  :  6.598  61.528    566
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 18.33 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.39), residues: 492
  helix:  1.72 (0.27), residues: 369
  sheet:  0.42 (1.41), residues: 10
  loop :  0.85 (0.66), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.021   0.002   TRP A 213 
 HIS   0.002   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3983)
  covalent geometry    : angle       0.47213 ( 5419)
  SS BOND              : bond        0.00596 (    2)
  SS BOND              : angle       0.70701 (    4)
  hydrogen bonds       : bond        0.04154 (  272)
  hydrogen bonds       : angle       4.12131 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 ASN cc_start: 0.7559 (m-40) cc_final: 0.7092 (t0)
REVERT: A  386 PHE cc_start: 0.7037 (m-10) cc_final: 0.6209 (t80)
REVERT: A  431 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7738 (tmtm)
  outliers start: 19
  outliers final: 10
  residues processed: 74
  average time/residue: 0.4448
  time to fit residues: 34.2491
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.5182

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.170810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.129958 restraints weight = 4444.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.07
r_work: 0.3299 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3985  Z= 0.145
  Angle     :  0.524   9.069   5423  Z= 0.259
  Chirality :  0.038   0.126    631
  Planarity :  0.003   0.025    673
  Dihedral  :  6.764  64.564    566
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.90 %
    Favored  : 78.33 %
  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 (0.39), residues: 492
  helix:  1.60 (0.27), residues: 368
  sheet:  0.46 (1.53), residues: 10
  loop :  0.77 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.018   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.024   0.002   TRP A 213 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3983)
  covalent geometry    : angle       0.52388 ( 5419)
  SS BOND              : bond        0.00878 (    2)
  SS BOND              : angle       0.89210 (    4)
  hydrogen bonds       : bond        0.04455 (  272)
  hydrogen bonds       : angle       4.19562 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 ASN cc_start: 0.7547 (m-40) cc_final: 0.7129 (t0)
REVERT: A    6 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6138 (mm)
REVERT: A  207 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5474 (tpt)
REVERT: A  386 PHE cc_start: 0.7192 (m-10) cc_final: 0.6347 (t80)
REVERT: A  431 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7731 (tmtm)
  outliers start: 20
  outliers final: 11
  residues processed: 75
  average time/residue: 0.4187
  time to fit residues: 32.7312
Evaluate side-chains
  71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0370
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.175210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.134396 restraints weight = 4464.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.11
r_work: 0.3342 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3985  Z= 0.113
  Angle     :  0.480   5.078   5423  Z= 0.240
  Chirality :  0.036   0.124    631
  Planarity :  0.003   0.024    673
  Dihedral  :  6.659  60.542    566
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.10 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.39), residues: 492
  helix:  1.67 (0.27), residues: 378
  sheet:  0.21 (1.57), residues: 10
  loop :  0.66 (0.67), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.013   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.028   0.002   TRP A 213 
 HIS   0.002   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3983)
  covalent geometry    : angle       0.47953 ( 5419)
  SS BOND              : bond        0.00524 (    2)
  SS BOND              : angle       0.71017 (    4)
  hydrogen bonds       : bond        0.04019 (  272)
  hydrogen bonds       : angle       4.04286 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5476 (tpt)
REVERT: A  386 PHE cc_start: 0.7074 (m-10) cc_final: 0.6268 (t80)
REVERT: A  431 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7737 (tmtt)
  outliers start: 17
  outliers final: 9
  residues processed: 71
  average time/residue: 0.4628
  time to fit residues: 34.1925
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.175181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134326 restraints weight = 4378.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.09
r_work: 0.3371 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3985  Z= 0.115
  Angle     :  0.515   9.517   5423  Z= 0.250
  Chirality :  0.037   0.125    631
  Planarity :  0.003   0.025    673
  Dihedral  :  6.637  60.712    566
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.81 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.39), residues: 492
  helix:  1.71 (0.27), residues: 378
  sheet:  0.21 (1.70), residues: 10
  loop :  0.73 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.014   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.033   0.002   TRP A 213 
 HIS   0.002   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3983)
  covalent geometry    : angle       0.51462 ( 5419)
  SS BOND              : bond        0.00567 (    2)
  SS BOND              : angle       0.72025 (    4)
  hydrogen bonds       : bond        0.03998 (  272)
  hydrogen bonds       : angle       4.02680 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5483 (tpt)
REVERT: A  386 PHE cc_start: 0.7094 (m-10) cc_final: 0.6285 (t80)
REVERT: A  431 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7774 (tmtm)
  outliers start: 14
  outliers final: 10
  residues processed: 67
  average time/residue: 0.4513
  time to fit residues: 31.5353
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:   10.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.173084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132442 restraints weight = 4425.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.08
r_work: 0.3316 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3985  Z= 0.135
  Angle     :  0.510   5.415   5423  Z= 0.255
  Chirality :  0.038   0.128    631
  Planarity :  0.004   0.026    673
  Dihedral  :  6.748  62.828    566
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.81 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.39), residues: 492
  helix:  1.62 (0.27), residues: 378
  sheet:  0.30 (1.76), residues: 10
  loop :  0.71 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.039   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3983)
  covalent geometry    : angle       0.50996 ( 5419)
  SS BOND              : bond        0.00745 (    2)
  SS BOND              : angle       0.81073 (    4)
  hydrogen bonds       : bond        0.04221 (  272)
  hydrogen bonds       : angle       4.09940 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5480 (tpt)
REVERT: A  212 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6425 (mt-10)
REVERT: A  386 PHE cc_start: 0.7165 (m-10) cc_final: 0.6308 (t80)
REVERT: A  431 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7739 (tmtm)
  outliers start: 17
  outliers final: 10
  residues processed: 72
  average time/residue: 0.4345
  time to fit residues: 32.6050
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.172930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.132088 restraints weight = 4374.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.08
r_work: 0.3323 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3985  Z= 0.128
  Angle     :  0.528   9.826   5423  Z= 0.260
  Chirality :  0.037   0.128    631
  Planarity :  0.004   0.025    673
  Dihedral  :  6.761  62.117    566
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.76 %
    Favored  : 76.90 %
  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:  2.06 (0.39), residues: 492
  helix:  1.63 (0.27), residues: 378
  sheet:  0.09 (1.70), residues: 10
  loop :  0.77 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.014   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.048   0.003   TRP A 213 
 HIS   0.002   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3983)
  covalent geometry    : angle       0.52791 ( 5419)
  SS BOND              : bond        0.00677 (    2)
  SS BOND              : angle       0.80295 (    4)
  hydrogen bonds       : bond        0.04143 (  272)
  hydrogen bonds       : angle       4.08489 (  801)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5485 (tpt)
REVERT: A  212 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6352 (mt-10)
REVERT: A  273 ARG cc_start: 0.6618 (ttm170) cc_final: 0.6333 (mtm180)
REVERT: A  328 GLU cc_start: 0.6611 (tp30) cc_final: 0.6402 (tp30)
REVERT: A  386 PHE cc_start: 0.7136 (m-10) cc_final: 0.6315 (t80)
REVERT: A  431 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7760 (tmtm)
  outliers start: 14
  outliers final: 10
  residues processed: 69
  average time/residue: 0.4782
  time to fit residues: 34.3425
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 THR
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0970
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.5716

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.175648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135087 restraints weight = 4308.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.07
r_work: 0.3361 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3985  Z= 0.110
  Angle     :  0.485   5.473   5423  Z= 0.242
  Chirality :  0.036   0.127    631
  Planarity :  0.003   0.026    673
  Dihedral  :  6.697  59.347    566
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.48 %
    Favored  : 76.67 %
  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:  2.22 (0.39), residues: 492
  helix:  1.74 (0.27), residues: 378
  sheet: -0.14 (1.59), residues: 10
  loop :  0.90 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.013   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.047   0.002   TRP A 213 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 3983)
  covalent geometry    : angle       0.48439 ( 5419)
  SS BOND              : bond        0.00465 (    2)
  SS BOND              : angle       0.68184 (    4)
  hydrogen bonds       : bond        0.03857 (  272)
  hydrogen bonds       : angle       3.98751 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1549.90 seconds
wall clock time: 27 minutes 16.61 seconds (1636.61 seconds total)