Starting phenix.real_space_refine
on Tue Feb  3 17:27:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gye_51693/02_2026/9gye_51693.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gye_51693/02_2026/9gye_51693.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gye_51693/02_2026/9gye_51693.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gye_51693/02_2026/9gye_51693.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gye_51693/02_2026/9gye_51693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gye_51693/02_2026/9gye_51693.map"
  }
  resolution = 3.5
  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=  -0.002 sd=   0.013
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       1      5.49       5
     S      16      5.16       5
     C    3481      2.51       5
     N     968      2.21       5
     O    1035      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5502
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 686, 5501
          Classifications: {'peptide': 686}
          Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 641}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.28, per 1000 atoms: 0.23
  Number of scatterers: 5502
  At special positions: 0
  Unit cell: (67.15, 73.1, 100.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      16     16.00
     P       1     15.00
     O    1035      8.00
     N     968      7.00
     C    3481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 306.1 milliseconds
  

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1260

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 7 sheets defined
      25.5% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 63 through 69
      removed outlier: 3.746A  pdb=" N   TYR A  67 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 4.086A  pdb=" N   VAL A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLN A 141 " --> pdb=" O   TRP A 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 136 through 141'
    Processing helix  chain 'A' and resid 142 through 145
    Processing helix  chain 'A' and resid 154 through 164
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.813A  pdb=" N   ASN A 181 " --> pdb=" O   PRO A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 229
    Processing helix  chain 'A' and resid 244 through 249
    Processing helix  chain 'A' and resid 267 through 271
      removed outlier: 3.707A  pdb=" N   TRP A 271 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
    Processing helix  chain 'A' and resid 282 through 288
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 325 through 341
      removed outlier: 3.728A  pdb=" N   GLY A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 348
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 3.968A  pdb=" N   LEU A 427 " --> pdb=" O   HIS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 449
    Processing helix  chain 'A' and resid 467 through 472
      removed outlier: 3.791A  pdb=" N   THR A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 488
      removed outlier: 3.946A  pdb=" N   SER A 476 " --> pdb=" O   ASN A 472 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE A 488 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 626
      removed outlier: 3.817A  pdb=" N   GLN A 625 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   MET A 626 " --> pdb=" O   ALA A 623 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 235
      removed outlier: 6.570A  pdb=" N   VAL A  54 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   ILE A 312 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ILE A  56 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LEU A 404 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 165 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   LEU A 166 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   VAL A 416 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95
    Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104
      removed outlier: 6.320A  pdb=" N   TYR A 103 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 526
    Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 572
    Processing sheet with id=AA6, first strand: chain 'A' and resid 576 through 577
    Processing sheet with id=AA7, first strand: chain 'A' and resid 629 through 635

    163 hydrogen bonds defined for protein.
    441 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: 0.87

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1835
        1.34 -     1.46: 1180
        1.46 -     1.57: 2629
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 5671
  Sorted by residual:
  bond pdb=" N   MET A 205 "
       pdb=" CA  MET A 205 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.23e-02 6.61e+03 5.85e+00
  bond pdb=" C   MET A 205 "
       pdb=" O   MET A 205 "
    ideal  model  delta    sigma   weight residual
    1.234  1.250 -0.016 1.19e-02 7.06e+03 1.79e+00
  bond pdb=" CA  ASP A 198 "
       pdb=" CB  ASP A 198 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.26e+00
  bond pdb=" C   VAL A 250 "
       pdb=" O   VAL A 250 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.25e+00
  bond pdb=" CA  MET A 289 "
       pdb=" CB  MET A 289 "
    ideal  model  delta    sigma   weight residual
    1.528  1.512  0.017 1.51e-02 4.39e+03 1.24e+00
  ... (remaining 5666 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 7496
        1.79 -     3.58: 189
        3.58 -     5.38: 40
        5.38 -     7.17: 8
        7.17 -     8.96: 5
  Bond angle restraints: 7738
  Sorted by residual:
  angle pdb=" CA  LYS A 494 "
        pdb=" CB  LYS A 494 "
        pdb=" CG  LYS A 494 "
      ideal   model   delta    sigma   weight residual
     114.10  121.94   -7.84 2.00e+00 2.50e-01 1.54e+01
  angle pdb=" CA  LYS A  97 "
        pdb=" CB  LYS A  97 "
        pdb=" CG  LYS A  97 "
      ideal   model   delta    sigma   weight residual
     114.10  119.92   -5.82 2.00e+00 2.50e-01 8.46e+00
  angle pdb=" N   ASN A 704 "
        pdb=" CA  ASN A 704 "
        pdb=" CB  ASN A 704 "
      ideal   model   delta    sigma   weight residual
     113.65  109.39    4.26 1.47e+00 4.63e-01 8.40e+00
  angle pdb=" CB  LYS A 494 "
        pdb=" CG  LYS A 494 "
        pdb=" CD  LYS A 494 "
      ideal   model   delta    sigma   weight residual
     111.30  117.88   -6.58 2.30e+00 1.89e-01 8.19e+00
  angle pdb=" N   LYS A  97 "
        pdb=" CA  LYS A  97 "
        pdb=" CB  LYS A  97 "
      ideal   model   delta    sigma   weight residual
     110.49  115.28   -4.79 1.69e+00 3.50e-01 8.02e+00
  ... (remaining 7733 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 2805
       17.48 -    34.97: 371
       34.97 -    52.45: 79
       52.45 -    69.93: 29
       69.93 -    87.41: 11
  Dihedral angle restraints: 3295
    sinusoidal: 1311
      harmonic: 1984
  Sorted by residual:
  dihedral pdb=" CA  ALA A 288 "
           pdb=" C   ALA A 288 "
           pdb=" N   MET A 289 "
           pdb=" CA  MET A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  GLN A 625 "
           pdb=" C   GLN A 625 "
           pdb=" N   MET A 626 "
           pdb=" CA  MET A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  TYR A 518 "
           pdb=" C   TYR A 518 "
           pdb=" N   GLN A 519 "
           pdb=" CA  GLN A 519 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.99   17.01     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 3292 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 643
       0.060 -    0.120: 129
       0.120 -    0.180: 10
       0.180 -    0.239: 1
       0.239 -    0.299: 1
  Chirality restraints: 784
  Sorted by residual:
  chirality pdb=" CG  LEU A 258 "
            pdb=" CB  LEU A 258 "
            pdb=" CD1 LEU A 258 "
            pdb=" CD2 LEU A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  ASP A 198 "
            pdb=" N   ASP A 198 "
            pdb=" C   ASP A 198 "
            pdb=" CB  ASP A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" CA  LYS A  97 "
            pdb=" N   LYS A  97 "
            pdb=" C   LYS A  97 "
            pdb=" CB  LYS A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.90e-01
  ... (remaining 781 not shown)

  Planarity restraints: 1025
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 674 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO A 675 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 675 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 675 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 257 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   ARG A 257 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ARG A 257 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 258 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 246 "   -0.009 2.00e-02 2.50e+03   9.68e-03 2.34e+00
        pdb=" CG  TRP A 246 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 246 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 246 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 246 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 246 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 246 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 246 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 246 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 246 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1022 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 157
        2.66 -     3.22: 5288
        3.22 -     3.78: 8896
        3.78 -     4.34: 11810
        4.34 -     4.90: 19469
  Nonbonded interactions: 45620
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 249 "
            pdb=" OH  TYR A 264 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OD1 ASN A  61 "
            pdb=" OD2 ASP A 360 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NH1 ARG A 287 "
     model   vdw
     2.120 3.120
  nonbonded pdb=" NE2 GLN A 236 "
            pdb=" O   GLY A 238 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OG1 THR A 110 "
            pdb=" O   PRO A 491 "
     model   vdw
     2.168 3.040
  ... (remaining 45615 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.960
  Find NCS groups from input model:        0.030
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5671  Z= 0.192
  Angle     :  0.737   8.961   7738  Z= 0.383
  Chirality :  0.048   0.299    784
  Planarity :  0.005   0.050   1025
  Dihedral  : 17.510  87.415   2035
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 30.43 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -0.21 (0.33), residues: 681
  helix:  0.41 (0.47), residues: 126
  sheet:  0.40 (0.41), residues: 174
  loop : -0.54 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 280 
 TYR   0.021   0.002   TYR A 318 
 PHE   0.008   0.001   PHE A 352 
 TRP   0.026   0.002   TRP A 246 
 HIS   0.005   0.001   HIS A 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 5671)
  covalent geometry    : angle       0.73737 ( 7738)
  hydrogen bonds       : bond        0.14976 (  163)
  hydrogen bonds       : angle       7.24828 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   58 MET cc_start: 0.7903 (ttt) cc_final: 0.7643 (ttm)
REVERT: A  146 MET cc_start: 0.7277 (mmm) cc_final: 0.7041 (mmm)
REVERT: A  237 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6274 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 52
  average time/residue: 0.0526
  time to fit residues: 3.9963
Evaluate side-chains
  38 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.053648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.044099 restraints weight = 24340.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.045905 restraints weight = 12099.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.047178 restraints weight = 7470.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.048081 restraints weight = 5244.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.048764 restraints weight = 3986.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5671  Z= 0.137
  Angle     :  0.607   6.946   7738  Z= 0.312
  Chirality :  0.045   0.245    784
  Planarity :  0.005   0.040   1025
  Dihedral  :  5.066  57.809    771
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 26.96 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.14 (0.33), residues: 681
  helix:  0.94 (0.49), residues: 125
  sheet:  0.70 (0.42), residues: 167
  loop : -0.43 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 646 
 TYR   0.021   0.002   TYR A 692 
 PHE   0.014   0.001   PHE A  68 
 TRP   0.015   0.001   TRP A 218 
 HIS   0.003   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5671)
  covalent geometry    : angle       0.60733 ( 7738)
  hydrogen bonds       : bond        0.03294 (  163)
  hydrogen bonds       : angle       5.52496 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 MET cc_start: 0.8260 (mmm) cc_final: 0.7436 (mmm)
REVERT: A  292 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7503 (ttt90)
REVERT: A  313 VAL cc_start: 0.9629 (t) cc_final: 0.9313 (p)
REVERT: A  496 TRP cc_start: 0.7599 (OUTLIER) cc_final: 0.6618 (m-90)
REVERT: A  540 ASP cc_start: 0.8294 (t0) cc_final: 0.8057 (t0)
REVERT: A  557 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8158 (mp10)
  outliers start: 21
  outliers final: 8
  residues processed: 58
  average time/residue: 0.0762
  time to fit residues: 5.8637
Evaluate side-chains
  47 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0570
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
A 475 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.054502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.045017 restraints weight = 24070.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.046834 restraints weight = 11856.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.048183 restraints weight = 7309.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.049098 restraints weight = 5025.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.049769 restraints weight = 3806.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5671  Z= 0.098
  Angle     :  0.538   6.204   7738  Z= 0.274
  Chirality :  0.044   0.194    784
  Planarity :  0.004   0.054   1025
  Dihedral  :  4.767  57.844    771
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.39 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.18 (0.33), residues: 681
  helix:  0.67 (0.47), residues: 137
  sheet:  0.80 (0.42), residues: 167
  loop : -0.36 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 241 
 TYR   0.023   0.001   TYR A 692 
 PHE   0.014   0.001   PHE A 100 
 TRP   0.015   0.001   TRP A 218 
 HIS   0.003   0.001   HIS A 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 5671)
  covalent geometry    : angle       0.53842 ( 7738)
  hydrogen bonds       : bond        0.02819 (  163)
  hydrogen bonds       : angle       5.13458 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.7628 (t-100)
REVERT: A  146 MET cc_start: 0.8304 (mmm) cc_final: 0.7164 (mmm)
REVERT: A  313 VAL cc_start: 0.9600 (t) cc_final: 0.9246 (p)
REVERT: A  332 TYR cc_start: 0.9146 (t80) cc_final: 0.8742 (t80)
REVERT: A  496 TRP cc_start: 0.7594 (OUTLIER) cc_final: 0.6647 (m-90)
REVERT: A  507 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8683 (mm-30)
REVERT: A  540 ASP cc_start: 0.8323 (t0) cc_final: 0.8000 (t0)
REVERT: A  720 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7462 (mtp85)
  outliers start: 19
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0489
  time to fit residues: 3.8786
Evaluate side-chains
  47 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  507 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0970
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
A 321 HIS
A 475 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.053760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.044348 restraints weight = 24719.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.046143 restraints weight = 12251.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.047414 restraints weight = 7608.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.048357 restraints weight = 5325.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.048999 restraints weight = 4016.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5671  Z= 0.130
  Angle     :  0.527   7.795   7738  Z= 0.269
  Chirality :  0.044   0.159    784
  Planarity :  0.004   0.055   1025
  Dihedral  :  4.734  57.992    771
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.65 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.31 (0.34), residues: 681
  helix:  0.83 (0.47), residues: 137
  sheet:  0.91 (0.42), residues: 167
  loop : -0.31 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 189 
 TYR   0.023   0.001   TYR A 692 
 PHE   0.009   0.001   PHE A  64 
 TRP   0.014   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5671)
  covalent geometry    : angle       0.52706 ( 7738)
  hydrogen bonds       : bond        0.02726 (  163)
  hydrogen bonds       : angle       5.11791 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 32
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  122 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7611 (t-100)
REVERT: A  125 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8677 (t80)
REVERT: A  138 MET cc_start: 0.7908 (mtp) cc_final: 0.7609 (ttm)
REVERT: A  146 MET cc_start: 0.8374 (mmm) cc_final: 0.7114 (mmm)
REVERT: A  292 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7613 (ttt90)
REVERT: A  332 TYR cc_start: 0.9184 (t80) cc_final: 0.8733 (t80)
REVERT: A  496 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.6663 (m-90)
REVERT: A  507 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8702 (mm-30)
REVERT: A  540 ASP cc_start: 0.8404 (t0) cc_final: 0.8030 (t0)
REVERT: A  557 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8015 (mp10)
REVERT: A  720 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7605 (mtp85)
  outliers start: 22
  outliers final: 5
  residues processed: 51
  average time/residue: 0.0668
  time to fit residues: 4.7537
Evaluate side-chains
  41 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  507 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3134 r_free = 0.3134 target = 0.053615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.044273 restraints weight = 24946.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.046039 restraints weight = 12210.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.047343 restraints weight = 7534.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.048240 restraints weight = 5220.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.048916 restraints weight = 3935.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5671  Z= 0.124
  Angle     :  0.524   6.626   7738  Z= 0.266
  Chirality :  0.043   0.142    784
  Planarity :  0.004   0.055   1025
  Dihedral  :  4.680  57.871    771
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 24.17 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.33 (0.34), residues: 681
  helix:  0.92 (0.47), residues: 137
  sheet:  0.91 (0.42), residues: 167
  loop : -0.33 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 189 
 TYR   0.024   0.001   TYR A 692 
 PHE   0.007   0.001   PHE A  64 
 TRP   0.015   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5671)
  covalent geometry    : angle       0.52402 ( 7738)
  hydrogen bonds       : bond        0.02647 (  163)
  hydrogen bonds       : angle       4.97427 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 33
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 TRP cc_start: 0.8225 (OUTLIER) cc_final: 0.7480 (t-100)
REVERT: A  125 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8680 (t80)
REVERT: A  138 MET cc_start: 0.8007 (mtp) cc_final: 0.7710 (ttm)
REVERT: A  174 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8666 (tmm)
REVERT: A  184 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8105 (t80)
REVERT: A  292 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7632 (ttt90)
REVERT: A  332 TYR cc_start: 0.9226 (t80) cc_final: 0.8758 (t80)
REVERT: A  496 TRP cc_start: 0.7641 (OUTLIER) cc_final: 0.6670 (m-90)
REVERT: A  507 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8697 (mm-30)
REVERT: A  540 ASP cc_start: 0.8428 (t0) cc_final: 0.8027 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0678
  time to fit residues: 5.1488
Evaluate side-chains
  49 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 32
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  184 TYR
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  507 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0870
   overall best weight:    1.5562

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

Flipped N/Q/H residues before XYZ refinement:
A 475 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.053109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.043653 restraints weight = 25069.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.045424 restraints weight = 12355.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.046707 restraints weight = 7661.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.047414 restraints weight = 5330.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.048195 restraints weight = 4185.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5671  Z= 0.123
  Angle     :  0.520   6.806   7738  Z= 0.263
  Chirality :  0.044   0.308    784
  Planarity :  0.004   0.054   1025
  Dihedral  :  4.655  57.473    771
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.13 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.37 (0.34), residues: 681
  helix:  0.95 (0.48), residues: 137
  sheet:  0.93 (0.43), residues: 161
  loop : -0.26 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 189 
 TYR   0.024   0.001   TYR A 692 
 PHE   0.006   0.001   PHE A  64 
 TRP   0.015   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5671)
  covalent geometry    : angle       0.51953 ( 7738)
  hydrogen bonds       : bond        0.02674 (  163)
  hydrogen bonds       : angle       4.96617 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 31
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7436 (t-100)
REVERT: A  125 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8700 (t80)
REVERT: A  138 MET cc_start: 0.8006 (mtp) cc_final: 0.7770 (ttm)
REVERT: A  184 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8115 (t80)
REVERT: A  292 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7702 (ttt90)
REVERT: A  332 TYR cc_start: 0.9294 (t80) cc_final: 0.8776 (t80)
REVERT: A  496 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.6696 (m-90)
REVERT: A  507 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8739 (mm-30)
REVERT: A  540 ASP cc_start: 0.8450 (t0) cc_final: 0.8037 (t0)
REVERT: A  557 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8026 (mp10)
  outliers start: 22
  outliers final: 11
  residues processed: 52
  average time/residue: 0.0530
  time to fit residues: 3.9494
Evaluate side-chains
  48 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 30
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  184 TYR
Chi-restraints excluded: chain A residue  292 ARG
Chi-restraints excluded: chain A residue  357 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  507 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  664 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.050483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.041498 restraints weight = 26140.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.043154 restraints weight = 13018.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.044342 restraints weight = 8108.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.045215 restraints weight = 5677.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.045798 restraints weight = 4312.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5671  Z= 0.296
  Angle     :  0.634   6.271   7738  Z= 0.329
  Chirality :  0.047   0.303    784
  Planarity :  0.005   0.046   1025
  Dihedral  :  5.212  57.924    771
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.78 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.09 (0.35), residues: 681
  helix:  0.55 (0.46), residues: 143
  sheet:  0.50 (0.44), residues: 158
  loop : -0.24 (0.35), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 189 
 TYR   0.025   0.002   TYR A 692 
 PHE   0.013   0.002   PHE A 556 
 TRP   0.020   0.002   TRP A 122 
 HIS   0.006   0.002   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 ( 5671)
  covalent geometry    : angle       0.63375 ( 7738)
  hydrogen bonds       : bond        0.03572 (  163)
  hydrogen bonds       : angle       5.44613 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 30
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  122 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7228 (t-100)
REVERT: A  125 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8817 (t80)
REVERT: A  138 MET cc_start: 0.8204 (mtp) cc_final: 0.7932 (ttm)
REVERT: A  174 MET cc_start: 0.8554 (tmm) cc_final: 0.8161 (tmm)
REVERT: A  496 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.6878 (m-90)
REVERT: A  540 ASP cc_start: 0.8501 (t0) cc_final: 0.8073 (t0)
REVERT: A  542 MET cc_start: 0.7965 (tpt) cc_final: 0.7682 (tpp)
REVERT: A  557 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8173 (mp10)
  outliers start: 25
  outliers final: 16
  residues processed: 53
  average time/residue: 0.0467
  time to fit residues: 3.8287
Evaluate side-chains
  49 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 29
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  253 TYR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  695 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.051125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.042069 restraints weight = 25586.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.043770 restraints weight = 12734.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.044945 restraints weight = 7883.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.045836 restraints weight = 5526.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.046458 restraints weight = 4190.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5671  Z= 0.213
  Angle     :  0.585   6.988   7738  Z= 0.300
  Chirality :  0.045   0.251    784
  Planarity :  0.004   0.047   1025
  Dihedral  :  5.073  57.765    771
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.13 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -0.11 (0.34), residues: 681
  helix:  0.54 (0.46), residues: 143
  sheet:  0.54 (0.45), residues: 142
  loop : -0.50 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 189 
 TYR   0.026   0.002   TYR A 692 
 PHE   0.010   0.001   PHE A 556 
 TRP   0.018   0.001   TRP A 122 
 HIS   0.005   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 5671)
  covalent geometry    : angle       0.58525 ( 7738)
  hydrogen bonds       : bond        0.03226 (  163)
  hydrogen bonds       : angle       5.34849 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 28
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.7233 (t-100)
REVERT: A  125 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8775 (t80)
REVERT: A  138 MET cc_start: 0.8159 (mtp) cc_final: 0.7913 (ttm)
REVERT: A  496 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.6820 (m-90)
REVERT: A  540 ASP cc_start: 0.8485 (t0) cc_final: 0.8057 (t0)
REVERT: A  542 MET cc_start: 0.7981 (tpt) cc_final: 0.7675 (tpp)
REVERT: A  557 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8148 (mp10)
  outliers start: 22
  outliers final: 17
  residues processed: 49
  average time/residue: 0.0652
  time to fit residues: 4.6090
Evaluate side-chains
  48 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 27
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  253 TYR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.052083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.042754 restraints weight = 25348.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.044500 restraints weight = 12584.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.045759 restraints weight = 7778.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.046639 restraints weight = 5413.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.047249 restraints weight = 4106.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5671  Z= 0.126
  Angle     :  0.543   7.045   7738  Z= 0.275
  Chirality :  0.044   0.222    784
  Planarity :  0.004   0.049   1025
  Dihedral  :  4.780  56.772    771
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.83 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole:  0.04 (0.34), residues: 681
  helix:  0.74 (0.48), residues: 143
  sheet:  0.71 (0.44), residues: 149
  loop : -0.49 (0.34), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 189 
 TYR   0.025   0.001   TYR A 692 
 PHE   0.006   0.001   PHE A 556 
 TRP   0.015   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5671)
  covalent geometry    : angle       0.54315 ( 7738)
  hydrogen bonds       : bond        0.02757 (  163)
  hydrogen bonds       : angle       5.07992 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 30
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7333 (t-100)
REVERT: A  125 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8784 (t80)
REVERT: A  138 MET cc_start: 0.7993 (mtp) cc_final: 0.7785 (ttm)
REVERT: A  496 TRP cc_start: 0.7587 (OUTLIER) cc_final: 0.6668 (m-90)
REVERT: A  540 ASP cc_start: 0.8470 (t0) cc_final: 0.8040 (t0)
REVERT: A  542 MET cc_start: 0.7959 (tpt) cc_final: 0.7634 (tpp)
REVERT: A  557 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8090 (mp10)
  outliers start: 17
  outliers final: 11
  residues processed: 46
  average time/residue: 0.0696
  time to fit residues: 4.6148
Evaluate side-chains
  44 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 29
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 34 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0000
   chunk 57 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    2.6590

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

Flipped N/Q/H residues before XYZ refinement:
** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.051109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.041952 restraints weight = 25815.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.043633 restraints weight = 12842.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.044851 restraints weight = 7980.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.045713 restraints weight = 5564.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.046359 restraints weight = 4230.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5671  Z= 0.192
  Angle     :  0.585   7.243   7738  Z= 0.296
  Chirality :  0.045   0.229    784
  Planarity :  0.004   0.047   1025
  Dihedral  :  4.940  56.709    771
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.35 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -0.05 (0.34), residues: 681
  helix:  0.66 (0.47), residues: 143
  sheet:  0.57 (0.45), residues: 142
  loop : -0.49 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 189 
 TYR   0.025   0.002   TYR A 692 
 PHE   0.009   0.001   PHE A 556 
 TRP   0.017   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 5671)
  covalent geometry    : angle       0.58472 ( 7738)
  hydrogen bonds       : bond        0.03034 (  163)
  hydrogen bonds       : angle       5.22538 (  441)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 28
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7322 (t-100)
REVERT: A  125 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8753 (t80)
REVERT: A  138 MET cc_start: 0.8128 (mtp) cc_final: 0.7891 (ttm)
REVERT: A  496 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6798 (m-90)
REVERT: A  507 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8683 (mm-30)
REVERT: A  540 ASP cc_start: 0.8512 (t0) cc_final: 0.8112 (t0)
REVERT: A  542 MET cc_start: 0.7992 (tpt) cc_final: 0.7674 (tpp)
REVERT: A  557 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8150 (mp10)
  outliers start: 17
  outliers final: 11
  residues processed: 45
  average time/residue: 0.0678
  time to fit residues: 4.4284
Evaluate side-chains
  44 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 28
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  122 TRP
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  496 TRP
Chi-restraints excluded: chain A residue  507 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  572 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  720 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.051993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.042736 restraints weight = 25176.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.044460 restraints weight = 12489.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.045672 restraints weight = 7736.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.046583 restraints weight = 5419.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.047190 restraints weight = 4087.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5671  Z= 0.136
  Angle     :  0.558   7.256   7738  Z= 0.280
  Chirality :  0.044   0.212    784
  Planarity :  0.004   0.048   1025
  Dihedral  :  4.789  56.269    771
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.52 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -0.03 (0.34), residues: 681
  helix:  0.73 (0.47), residues: 143
  sheet:  0.66 (0.44), residues: 149
  loop : -0.55 (0.34), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 646 
 TYR   0.024   0.001   TYR A 692 
 PHE   0.006   0.001   PHE A 556 
 TRP   0.016   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5671)
  covalent geometry    : angle       0.55798 ( 7738)
  hydrogen bonds       : bond        0.02788 (  163)
  hydrogen bonds       : angle       5.07852 (  441)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1029.25 seconds
wall clock time: 18 minutes 30.20 seconds (1110.20 seconds total)