Starting phenix.real_space_refine
on Tue Mar  3 11:25:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cwo_30485/03_2026/7cwo_30485.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cwo_30485/03_2026/7cwo_30485.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2026/7cwo_30485.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2026/7cwo_30485.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2026/7cwo_30485.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2026/7cwo_30485.map"
  }
  resolution = 3.9
  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      14      5.16       5
     C    2063      2.51       5
     N     558      2.21       5
     O     619      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3254
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1519
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "H"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 918
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 817
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101}
  Time building chain proxies: 0.81, per 1000 atoms: 0.25
  Number of scatterers: 3254
  At special positions: 0
  Unit cell: (84.24, 70.72, 84.24, 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      14     16.00
     O     619      8.00
     N     558      7.00
     C    2063      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.15
  Conformation dependent library (CDL) restraints added in 90.1 milliseconds
  

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 7 sheets defined
      10.7% alpha, 27.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 4.140A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ALA A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.910A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 385 through 389'
    Processing helix  chain 'A' and resid 405 through 409
      removed outlier: 3.952A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 506
      removed outlier: 3.675A  pdb=" N   GLN A 506 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 4.009A  pdb=" N   TYR A 473 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.550A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
      removed outlier: 11.870A  pdb=" N   CYS L  23 " --> pdb=" O   THR L  74 " (cutoff:3.500A)
      removed outlier: 10.398A  pdb=" N   THR L  74 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 11.550A  pdb=" N   ALA L  25 " --> pdb=" O   THR L  72 " (cutoff:3.500A)
      removed outlier: 11.278A  pdb=" N   THR L  72 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.345A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   ASP L  70 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.606A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    85 hydrogen bonds defined for protein.
    201 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: 0.55

  Time building geometry restraints manager: 0.20 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: 1028
        1.34 -     1.46: 879
        1.46 -     1.58: 1411
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3334
  Sorted by residual:
  bond pdb=" C   VAL H  12 "
       pdb=" N   GLN H  13 "
    ideal  model  delta    sigma   weight residual
    1.330  1.367 -0.037 1.47e-02 4.63e+03 6.43e+00
  bond pdb=" C   VAL A 433 "
       pdb=" N   ILE A 434 "
    ideal  model  delta    sigma   weight residual
    1.330  1.303  0.027 1.26e-02 6.30e+03 4.60e+00
  bond pdb=" C   SER L  93 "
       pdb=" N   THR L  94 "
    ideal  model  delta    sigma   weight residual
    1.332  1.296  0.036 1.92e-02 2.71e+03 3.54e+00
  bond pdb=" CG  GLN L  89 "
       pdb=" CD  GLN L  89 "
    ideal  model  delta    sigma   weight residual
    1.516  1.474  0.042 2.50e-02 1.60e+03 2.81e+00
  bond pdb=" CB  TRP H  47 "
       pdb=" CG  TRP H  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.447  0.051 3.10e-02 1.04e+03 2.67e+00
  ... (remaining 3329 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 4293
        2.11 -     4.23: 202
        4.23 -     6.34: 28
        6.34 -     8.46: 3
        8.46 -    10.57: 3
  Bond angle restraints: 4529
  Sorted by residual:
  angle pdb=" C   PHE A 486 "
        pdb=" N   ASN A 487 "
        pdb=" CA  ASN A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  130.56   -9.02 1.91e+00 2.74e-01 2.23e+01
  angle pdb=" C   GLN L  38 "
        pdb=" N   LYS L  39 "
        pdb=" CA  LYS L  39 "
      ideal   model   delta    sigma   weight residual
     120.49  114.65    5.84 1.42e+00 4.96e-01 1.69e+01
  angle pdb=" N   VAL A 382 "
        pdb=" CA  VAL A 382 "
        pdb=" C   VAL A 382 "
      ideal   model   delta    sigma   weight residual
     108.23  103.40    4.83 1.43e+00 4.89e-01 1.14e+01
  angle pdb=" N   MET H 103 "
        pdb=" CA  MET H 103 "
        pdb=" C   MET H 103 "
      ideal   model   delta    sigma   weight residual
     112.93  108.70    4.23 1.33e+00 5.65e-01 1.01e+01
  angle pdb=" C   PRO A 463 "
        pdb=" N   PHE A 464 "
        pdb=" CA  PHE A 464 "
      ideal   model   delta    sigma   weight residual
     123.05  127.97   -4.92 1.57e+00 4.06e-01 9.81e+00
  ... (remaining 4524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.80: 1685
        9.80 -    19.60: 223
       19.60 -    29.40: 43
       29.40 -    39.20: 12
       39.20 -    49.00: 7
  Dihedral angle restraints: 1970
    sinusoidal: 749
      harmonic: 1221
  Sorted by residual:
  dihedral pdb=" CA  ARG H  72 "
           pdb=" C   ARG H  72 "
           pdb=" N   ASP H  73 "
           pdb=" CA  ASP H  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.51   38.49     0      5.00e+00 4.00e-02 5.93e+01
  dihedral pdb=" CA  CYS A 391 "
           pdb=" C   CYS A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.21  -33.79     0      5.00e+00 4.00e-02 4.57e+01
  dihedral pdb=" CA  ARG H  87 "
           pdb=" C   ARG H  87 "
           pdb=" N   ALA H  88 "
           pdb=" CA  ALA H  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.61  -28.39     0      5.00e+00 4.00e-02 3.22e+01
  ... (remaining 1967 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 306
       0.047 -    0.093: 139
       0.093 -    0.140: 34
       0.140 -    0.187: 10
       0.187 -    0.233: 1
  Chirality restraints: 490
  Sorted by residual:
  chirality pdb=" CG  LEU H  79 "
            pdb=" CB  LEU H  79 "
            pdb=" CD1 LEU H  79 "
            pdb=" CD2 LEU H  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CB  VAL A 350 "
            pdb=" CA  VAL A 350 "
            pdb=" CG1 VAL A 350 "
            pdb=" CG2 VAL A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CB  ILE H  70 "
            pdb=" CA  ILE H  70 "
            pdb=" CG1 ILE H  70 "
            pdb=" CG2 ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 487 not shown)

  Planarity restraints: 585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  58 "   -0.034 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO L  59 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO L  59 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L  59 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 392 "   -0.017 2.00e-02 2.50e+03   1.54e-02 4.12e+00
        pdb=" CG  PHE A 392 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 392 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 392 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 392 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 392 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 392 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H 101 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.93e+00
        pdb=" C   THR H 101 "    0.034 2.00e-02 2.50e+03
        pdb=" O   THR H 101 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU H 102 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 582 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 832
        2.79 -     3.32: 2933
        3.32 -     3.84: 5385
        3.84 -     4.37: 6236
        4.37 -     4.90: 10594
  Nonbonded interactions: 25980
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OH  TYR A 369 "
            pdb=" O   PRO A 384 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OH  TYR L  36 "
            pdb=" OE1 GLN L  89 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   THR A 393 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OG1 THR A 393 "
            pdb=" OD1 ASN A 394 "
     model   vdw
     2.326 3.040
  ... (remaining 25975 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.680
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
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      :  0.007   0.060   3340  Z= 0.320
  Angle     :  1.044  10.573   4541  Z= 0.603
  Chirality :  0.057   0.233    490
  Planarity :  0.007   0.052    585
  Dihedral  :  9.374  43.259   1178
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.14 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

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: -3.72 (0.36), residues: 416
  helix: -4.84 (0.54), residues: 15
  sheet: -2.29 (0.40), residues: 141
  loop : -2.51 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  61 
 TYR   0.030   0.003   TYR H  94 
 PHE   0.035   0.004   PHE A 392 
 TRP   0.025   0.003   TRP H  47 
 HIS   0.005   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 ( 3334)
  covalent geometry    : angle       1.04388 ( 4529)
  SS BOND              : bond        0.00618 (    6)
  SS BOND              : angle       1.11340 (   12)
  hydrogen bonds       : bond        0.17390 (   85)
  hydrogen bonds       : angle      13.26128 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.6843 (mttp) cc_final: 0.6276 (tttt)
REVERT: H   45 LEU cc_start: 0.7485 (mt) cc_final: 0.7001 (mt)
REVERT: H   72 ARG cc_start: 0.7856 (ptt90) cc_final: 0.7263 (ptp-110)
REVERT: H   81 LEU cc_start: 0.9053 (tt) cc_final: 0.8709 (tp)
REVERT: L    4 LEU cc_start: 0.8811 (mt) cc_final: 0.8527 (mm)
REVERT: L   11 LEU cc_start: 0.7856 (tt) cc_final: 0.7409 (mt)
REVERT: L   82 ASP cc_start: 0.8034 (m-30) cc_final: 0.7113 (t0)
REVERT: L  104 VAL cc_start: 0.8817 (t) cc_final: 0.8451 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 116
  average time/residue: 0.0761
  time to fit residues: 10.1783
Evaluate side-chains
  66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0270
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 501 ASN
H  35 HIS
H  84 ASN
H 104 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.082255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.073195 restraints weight = 13995.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.075131 restraints weight = 7541.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.076477 restraints weight = 4768.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.077372 restraints weight = 3327.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.077932 restraints weight = 2520.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3340  Z= 0.177
  Angle     :  0.734   9.792   4541  Z= 0.380
  Chirality :  0.046   0.183    490
  Planarity :  0.005   0.041    585
  Dihedral  :  6.815  31.098    468
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.40 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

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: -3.25 (0.37), residues: 416
  helix: -4.37 (0.57), residues: 21
  sheet: -1.68 (0.41), residues: 135
  loop : -2.32 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  67 
 TYR   0.017   0.002   TYR L  49 
 PHE   0.016   0.002   PHE H  27 
 TRP   0.011   0.002   TRP L  35 
 HIS   0.003   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 3334)
  covalent geometry    : angle       0.71471 ( 4529)
  SS BOND              : bond        0.00444 (    6)
  SS BOND              : angle       3.33412 (   12)
  hydrogen bonds       : bond        0.03906 (   85)
  hydrogen bonds       : angle       9.41838 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.6853 (mttp) cc_final: 0.6576 (tttt)
REVERT: A  457 ARG cc_start: 0.6475 (ttt-90) cc_final: 0.6202 (ttt-90)
REVERT: A  492 LEU cc_start: 0.8954 (mm) cc_final: 0.8651 (mt)
REVERT: A  524 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8446 (p)
REVERT: H   72 ARG cc_start: 0.7412 (ptt90) cc_final: 0.7051 (ptp-110)
REVERT: H   74 ASN cc_start: 0.7985 (p0) cc_final: 0.7744 (p0)
REVERT: H   76 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8299 (ptmt)
REVERT: L  104 VAL cc_start: 0.8717 (t) cc_final: 0.8440 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 84
  average time/residue: 0.0686
  time to fit residues: 6.9980
Evaluate side-chains
  66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 30 optimal weight:    0.0980
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   chunk 11 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.3763 r_free = 0.3763 target = 0.084735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.075377 restraints weight = 13795.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.077407 restraints weight = 7471.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.078786 restraints weight = 4721.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.079733 restraints weight = 3324.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.080401 restraints weight = 2521.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3340  Z= 0.108
  Angle     :  0.660   7.564   4541  Z= 0.330
  Chirality :  0.046   0.185    490
  Planarity :  0.004   0.034    585
  Dihedral  :  5.739  25.788    468
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 13.96 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.77 (0.38), residues: 416
  helix: -4.30 (0.52), residues: 21
  sheet: -1.07 (0.44), residues: 129
  loop : -2.12 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  16 
 TYR   0.018   0.001   TYR L  92 
 PHE   0.016   0.001   PHE A 392 
 TRP   0.009   0.001   TRP L  35 
 HIS   0.002   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 3334)
  covalent geometry    : angle       0.64373 ( 4529)
  SS BOND              : bond        0.00547 (    6)
  SS BOND              : angle       2.93126 (   12)
  hydrogen bonds       : bond        0.03202 (   85)
  hydrogen bonds       : angle       7.82295 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.7141 (ptt90) cc_final: 0.6912 (ptp-110)
REVERT: H  103 MET cc_start: 0.7491 (mmm) cc_final: 0.7195 (mmm)
REVERT: L  104 VAL cc_start: 0.8500 (t) cc_final: 0.8203 (p)
  outliers start: 12
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0713
  time to fit residues: 7.5645
Evaluate side-chains
  63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:   20.0000
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.082482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.073271 restraints weight = 14264.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.075273 restraints weight = 7829.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.076558 restraints weight = 5028.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.077503 restraints weight = 3607.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.078136 restraints weight = 2744.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.4090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3340  Z= 0.165
  Angle     :  0.710  11.839   4541  Z= 0.357
  Chirality :  0.044   0.155    490
  Planarity :  0.005   0.033    585
  Dihedral  :  5.639  25.806    467
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.23 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.55 (0.38), residues: 416
  helix: -4.48 (0.64), residues: 15
  sheet: -1.17 (0.42), residues: 137
  loop : -1.87 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 457 
 TYR   0.023   0.002   TYR H  32 
 PHE   0.016   0.002   PHE A 392 
 TRP   0.015   0.002   TRP L  35 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3334)
  covalent geometry    : angle       0.69771 ( 4529)
  SS BOND              : bond        0.00280 (    6)
  SS BOND              : angle       2.66413 (   12)
  hydrogen bonds       : bond        0.03252 (   85)
  hydrogen bonds       : angle       7.62169 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  457 ARG cc_start: 0.6124 (ttt-90) cc_final: 0.5888 (ttt-90)
REVERT: H  103 MET cc_start: 0.7496 (mmm) cc_final: 0.7233 (mmm)
REVERT: L  104 VAL cc_start: 0.8488 (t) cc_final: 0.8197 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0647
  time to fit residues: 5.8477
Evaluate side-chains
  68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 105 ASN
L   3 GLN
L  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.079939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.070404 restraints weight = 14025.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.072380 restraints weight = 7612.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.073638 restraints weight = 4848.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.074533 restraints weight = 3477.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.075140 restraints weight = 2684.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   3340  Z= 0.245
  Angle     :  0.748  12.453   4541  Z= 0.384
  Chirality :  0.046   0.152    490
  Planarity :  0.005   0.034    585
  Dihedral  :  6.066  27.533    467
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.23 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.68 (0.37), residues: 416
  helix: -4.37 (0.68), residues: 15
  sheet: -1.34 (0.40), residues: 148
  loop : -1.93 (0.35), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  24 
 TYR   0.019   0.002   TYR H  53 
 PHE   0.012   0.002   PHE A 392 
 TRP   0.015   0.002   TRP L  35 
 HIS   0.005   0.002   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 3334)
  covalent geometry    : angle       0.73605 ( 4529)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       2.64971 (   12)
  hydrogen bonds       : bond        0.03787 (   85)
  hydrogen bonds       : angle       7.90488 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  492 LEU cc_start: 0.8808 (mm) cc_final: 0.8603 (mt)
REVERT: H  103 MET cc_start: 0.7694 (mmm) cc_final: 0.7342 (mmm)
REVERT: L  104 VAL cc_start: 0.8474 (t) cc_final: 0.8185 (p)
  outliers start: 15
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0638
  time to fit residues: 5.4280
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 5 optimal weight:    0.4980
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:   30.0000
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   3 GLN
** L  34 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 = 0.3675 r_free = 0.3675 target = 0.080210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.070561 restraints weight = 14086.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.072527 restraints weight = 7751.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.073828 restraints weight = 4972.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.074720 restraints weight = 3554.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.075280 restraints weight = 2745.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.4523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   3340  Z= 0.199
  Angle     :  0.708   8.770   4541  Z= 0.363
  Chirality :  0.046   0.206    490
  Planarity :  0.005   0.065    585
  Dihedral  :  5.843  26.083    467
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.23 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.45 (0.38), residues: 416
  helix: -4.33 (0.70), residues: 15
  sheet: -1.10 (0.41), residues: 150
  loop : -1.83 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  67 
 TYR   0.014   0.002   TYR L  49 
 PHE   0.015   0.002   PHE A 392 
 TRP   0.019   0.002   TRP L  35 
 HIS   0.005   0.002   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 3334)
  covalent geometry    : angle       0.69887 ( 4529)
  SS BOND              : bond        0.00425 (    6)
  SS BOND              : angle       2.35288 (   12)
  hydrogen bonds       : bond        0.03559 (   85)
  hydrogen bonds       : angle       8.00593 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  103 MET cc_start: 0.7632 (mmm) cc_final: 0.7256 (mmm)
  outliers start: 16
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0541
  time to fit residues: 4.5006
Evaluate side-chains
  65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0070
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.9758

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.083503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.074063 restraints weight = 14240.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.076044 restraints weight = 7663.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.077425 restraints weight = 4861.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.078321 restraints weight = 3440.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.078924 restraints weight = 2631.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3340  Z= 0.108
  Angle     :  0.655   9.123   4541  Z= 0.324
  Chirality :  0.045   0.182    490
  Planarity :  0.004   0.036    585
  Dihedral  :  5.092  20.471    467
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 21.37 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.25 (0.37), residues: 416
  helix: -4.36 (0.64), residues: 15
  sheet: -0.94 (0.40), residues: 151
  loop : -1.69 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  24 
 TYR   0.014   0.001   TYR L  49 
 PHE   0.018   0.001   PHE A 392 
 TRP   0.018   0.002   TRP L  35 
 HIS   0.002   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3334)
  covalent geometry    : angle       0.64945 ( 4529)
  SS BOND              : bond        0.00365 (    6)
  SS BOND              : angle       1.81269 (   12)
  hydrogen bonds       : bond        0.02947 (   85)
  hydrogen bonds       : angle       7.07016 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   54 ASP cc_start: 0.5516 (m-30) cc_final: 0.5230 (m-30)
REVERT: H  103 MET cc_start: 0.7576 (mmm) cc_final: 0.7210 (mmm)
REVERT: L   81 GLU cc_start: 0.7534 (pm20) cc_final: 0.7325 (pm20)
  outliers start: 12
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0650
  time to fit residues: 5.6369
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  35 HIS
L  27 GLN
L  34 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.083446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.073776 restraints weight = 14642.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.075764 restraints weight = 8042.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.077126 restraints weight = 5195.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.078054 restraints weight = 3739.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.078630 restraints weight = 2873.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3340  Z= 0.116
  Angle     :  0.685  11.832   4541  Z= 0.334
  Chirality :  0.045   0.170    490
  Planarity :  0.004   0.036    585
  Dihedral  :  4.936  19.917    467
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.51 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.09 (0.38), residues: 416
  helix: -4.38 (0.63), residues: 15
  sheet: -0.82 (0.40), residues: 151
  loop : -1.58 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  24 
 TYR   0.013   0.001   TYR L  49 
 PHE   0.017   0.001   PHE A 392 
 TRP   0.031   0.002   TRP L  35 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3334)
  covalent geometry    : angle       0.67999 ( 4529)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       1.72692 (   12)
  hydrogen bonds       : bond        0.02881 (   85)
  hydrogen bonds       : angle       6.84570 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   54 ASP cc_start: 0.5395 (m-30) cc_final: 0.5144 (m-30)
REVERT: H  103 MET cc_start: 0.7616 (mmm) cc_final: 0.7261 (mmm)
REVERT: L   81 GLU cc_start: 0.7521 (pm20) cc_final: 0.7269 (pm20)
  outliers start: 13
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0637
  time to fit residues: 5.2901
Evaluate side-chains
  64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   82 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.082227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072788 restraints weight = 14396.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.074743 restraints weight = 7798.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.076058 restraints weight = 4994.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.076905 restraints weight = 3552.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.077545 restraints weight = 2768.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3340  Z= 0.152
  Angle     :  0.708  12.047   4541  Z= 0.346
  Chirality :  0.045   0.163    490
  Planarity :  0.004   0.035    585
  Dihedral  :  5.183  20.847    467
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.79 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.02 (0.38), residues: 416
  helix: -4.31 (0.69), residues: 15
  sheet: -0.76 (0.41), residues: 153
  loop : -1.55 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  24 
 TYR   0.014   0.002   TYR L  49 
 PHE   0.015   0.001   PHE A 392 
 TRP   0.039   0.003   TRP L  35 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3334)
  covalent geometry    : angle       0.70231 ( 4529)
  SS BOND              : bond        0.00348 (    6)
  SS BOND              : angle       1.82586 (   12)
  hydrogen bonds       : bond        0.03210 (   85)
  hydrogen bonds       : angle       6.98704 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   54 ASP cc_start: 0.5514 (m-30) cc_final: 0.5192 (m-30)
REVERT: H  103 MET cc_start: 0.7694 (mmm) cc_final: 0.7323 (mmm)
  outliers start: 12
  outliers final: 12
  residues processed: 60
  average time/residue: 0.0611
  time to fit residues: 4.5672
Evaluate side-chains
  66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 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 = 0.3644 r_free = 0.3644 target = 0.079461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.069647 restraints weight = 14349.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.071596 restraints weight = 7896.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.072957 restraints weight = 5086.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.073865 restraints weight = 3639.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.074441 restraints weight = 2804.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.4971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   3340  Z= 0.276
  Angle     :  0.792  10.859   4541  Z= 0.406
  Chirality :  0.047   0.165    490
  Planarity :  0.004   0.034    585
  Dihedral  :  5.999  25.935    467
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 21.94 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.29 (0.38), residues: 416
  helix: -4.33 (0.68), residues: 15
  sheet: -1.06 (0.41), residues: 151
  loop : -1.66 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  24 
 TYR   0.014   0.002   TYR L  49 
 PHE   0.013   0.003   PHE A 392 
 TRP   0.050   0.004   TRP L  35 
 HIS   0.004   0.002   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 3334)
  covalent geometry    : angle       0.78497 ( 4529)
  SS BOND              : bond        0.00466 (    6)
  SS BOND              : angle       2.25673 (   12)
  hydrogen bonds       : bond        0.03999 (   85)
  hydrogen bonds       : angle       7.75315 (  201)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  492 LEU cc_start: 0.8783 (mm) cc_final: 0.8569 (mt)
REVERT: H  103 MET cc_start: 0.7818 (mmm) cc_final: 0.7396 (mmm)
  outliers start: 16
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0464
  time to fit residues: 3.7259
Evaluate side-chains
  65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.085613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.075901 restraints weight = 14787.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.077816 restraints weight = 8486.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.079104 restraints weight = 5660.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.079967 restraints weight = 4183.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.080615 restraints weight = 3329.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.5227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3340  Z= 0.126
  Angle     :  0.726  10.483   4541  Z= 0.356
  Chirality :  0.046   0.236    490
  Planarity :  0.004   0.032    585
  Dihedral  :  5.178  20.981    467
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.22 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.98 (0.39), residues: 416
  helix: -4.35 (0.63), residues: 15
  sheet: -0.81 (0.41), residues: 160
  loop : -1.46 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  24 
 TYR   0.038   0.002   TYR L  92 
 PHE   0.017   0.002   PHE A 392 
 TRP   0.043   0.003   TRP L  35 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3334)
  covalent geometry    : angle       0.72115 ( 4529)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       1.71071 (   12)
  hydrogen bonds       : bond        0.03294 (   85)
  hydrogen bonds       : angle       7.13995 (  201)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 725.02 seconds
wall clock time: 13 minutes 10.76 seconds (790.76 seconds total)