Starting phenix.real_space_refine
on Thu Mar  6 02:57:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cxo_27062/03_2025/8cxo_27062.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cxo_27062/03_2025/8cxo_27062.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2025/8cxo_27062.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2025/8cxo_27062.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2025/8cxo_27062.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2025/8cxo_27062.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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      30      5.16       5
     C    2863      2.51       5
     N     724      2.21       5
     O     775      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4392
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4364
          Classifications: {'peptide': 551}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 535}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.32, per 1000 atoms: 0.76
  Number of scatterers: 4392
  At special positions: 0
  Unit cell: (75.985, 65.13, 123.58, 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      30     16.00
     O     775      8.00
     N     724      7.00
     C    2863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 197 " - pdb=" SG  CYS A 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 221 " - pdb=" SG  CYS A 299 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 318 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 511 " distance=2.03

  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: 1.31
  Conformation dependent library (CDL) restraints added in 617.2 milliseconds
  

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1010

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 3 sheets defined
      65.5% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 227 through 259
      removed outlier: 3.998A  pdb=" N   ASP A 259 " --> pdb=" O   THR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 264
    Processing helix  chain 'A' and resid 265 through 268
    Processing helix  chain 'A' and resid 269 through 287
      removed outlier: 3.595A  pdb=" N   TYR A 273 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 290
      No H-bonds generated for 'chain 'A' and resid 288 through 290'
    Processing helix  chain 'A' and resid 292 through 299
    Processing helix  chain 'A' and resid 316 through 347
      removed outlier: 4.079A  pdb=" N   PHE A 347 " --> pdb=" O   TRP A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 360 through 382
      Proline residue:  A 372  - end of helix
      removed outlier: 3.526A  pdb=" N   VAL A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 408
      removed outlier: 3.825A  pdb=" N   ARG A 404 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 437
    Processing helix  chain 'A' and resid 1015 through 1027
    Processing helix  chain 'A' and resid 1047 through 1059
    Processing helix  chain 'A' and resid 1060 through 1065
      removed outlier: 6.464A  pdb=" N   GLU A1063 " --> pdb=" O   SER A1060 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLN A1065 " --> pdb=" O   LYS A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1090
    Processing helix  chain 'A' and resid 1101 through 1112
    Processing helix  chain 'A' and resid 1126 through 1134
      removed outlier: 4.036A  pdb=" N   GLU A1130 " --> pdb=" O   LEU A1126 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA A1131 " --> pdb=" O   VAL A1127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1149
      removed outlier: 4.029A  pdb=" N   ARG A1147 " --> pdb=" O   GLY A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1178
    Processing helix  chain 'A' and resid 1181 through 1193
    Processing helix  chain 'A' and resid 1206 through 452
      removed outlier: 3.526A  pdb=" N   GLU A 451 " --> pdb=" O   ALA A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 494
      removed outlier: 3.599A  pdb=" N   PHE A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ALA A 482 " --> pdb=" O   PHE A 478 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   GLU A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   CYS A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 497
      No H-bonds generated for 'chain 'A' and resid 495 through 497'
    Processing helix  chain 'A' and resid 518 through 537
      removed outlier: 3.690A  pdb=" N   GLY A 533 " --> pdb=" O   MET A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 541
    Processing helix  chain 'A' and resid 542 through 554
      removed outlier: 3.682A  pdb=" N   LEU A 546 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 203
    Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 388
      removed outlier: 3.551A  pdb=" N   ASP A 388 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE A 393 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1093 through 1096
      removed outlier: 5.722A  pdb=" N   VAL A1033 " --> pdb=" O   ARG A1068 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   ILE A1070 " --> pdb=" O   VAL A1033 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   PHE A1035 " --> pdb=" O   ILE A1070 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   ILE A1072 " --> pdb=" O   PHE A1035 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE A1037 " --> pdb=" O   ILE A1072 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   THR A1034 " --> pdb=" O   PHE A1114 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   ILE A1116 " --> pdb=" O   THR A1034 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   MET A1036 " --> pdb=" O   ILE A1116 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1374
        1.34 -     1.46: 1147
        1.46 -     1.58: 1935
        1.58 -     1.70: 0
        1.70 -     1.82: 45
  Bond restraints: 4501
  Sorted by residual:
  bond pdb=" C13 CLR A1301 "
       pdb=" C14 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.537  1.504  0.033 2.00e-02 2.50e+03 2.71e+00
  bond pdb=" C1  CLR A1301 "
       pdb=" C10 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.515  0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" C16 CLR A1301 "
       pdb=" C17 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.554  1.528  0.026 2.00e-02 2.50e+03 1.67e+00
  bond pdb=" C15 CLR A1301 "
       pdb=" C16 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.541  1.517  0.024 2.00e-02 2.50e+03 1.45e+00
  bond pdb=" CA  VAL A 214 "
       pdb=" CB  VAL A 214 "
    ideal  model  delta    sigma   weight residual
    1.527  1.541 -0.014 1.31e-02 5.83e+03 1.19e+00
  ... (remaining 4496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 5911
        1.39 -     2.77: 145
        2.77 -     4.16: 22
        4.16 -     5.54: 16
        5.54 -     6.93: 2
  Bond angle restraints: 6096
  Sorted by residual:
  angle pdb=" N   CYS A1004 "
        pdb=" CA  CYS A1004 "
        pdb=" C   CYS A1004 "
      ideal   model   delta    sigma   weight residual
     107.20  112.41   -5.21 1.70e+00 3.46e-01 9.41e+00
  angle pdb=" C   TYR A 211 "
        pdb=" N   GLU A 212 "
        pdb=" CA  GLU A 212 "
      ideal   model   delta    sigma   weight residual
     121.19  125.96   -4.77 1.59e+00 3.96e-01 8.98e+00
  angle pdb=" N   TYR A 266 "
        pdb=" CA  TYR A 266 "
        pdb=" C   TYR A 266 "
      ideal   model   delta    sigma   weight residual
     109.81  115.33   -5.52 2.21e+00 2.05e-01 6.24e+00
  angle pdb=" N   GLY A1001 "
        pdb=" CA  GLY A1001 "
        pdb=" C   GLY A1001 "
      ideal   model   delta    sigma   weight residual
     113.99  116.99   -3.00 1.28e+00 6.10e-01 5.50e+00
  angle pdb=" C6  CLR A1301 "
        pdb=" C7  CLR A1301 "
        pdb=" C8  CLR A1301 "
      ideal   model   delta    sigma   weight residual
     113.19  106.26    6.93 3.00e+00 1.11e-01 5.34e+00
  ... (remaining 6091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2541
       17.14 -    34.28: 110
       34.28 -    51.42: 20
       51.42 -    68.56: 3
       68.56 -    85.70: 1
  Dihedral angle restraints: 2675
    sinusoidal: 1098
      harmonic: 1577
  Sorted by residual:
  dihedral pdb=" CB  CYS A 494 "
           pdb=" SG  CYS A 494 "
           pdb=" SG  CYS A 511 "
           pdb=" CB  CYS A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.05  -52.05     1      1.00e+01 1.00e-02 3.70e+01
  dihedral pdb=" CA  LEU A 441 "
           pdb=" C   LEU A 441 "
           pdb=" N   GLY A1001 "
           pdb=" CA  GLY A1001 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.34  -29.66     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  TYR A 211 "
           pdb=" C   TYR A 211 "
           pdb=" N   GLU A 212 "
           pdb=" CA  GLU A 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 2672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 553
       0.045 -    0.089: 90
       0.089 -    0.134: 29
       0.134 -    0.178: 4
       0.178 -    0.223: 1
  Chirality restraints: 677
  Sorted by residual:
  chirality pdb=" C10 CLR A1301 "
            pdb=" C1  CLR A1301 "
            pdb=" C5  CLR A1301 "
            pdb=" C9  CLR A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.63   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  ILE A1139 "
            pdb=" N   ILE A1139 "
            pdb=" C   ILE A1139 "
            pdb=" CB  ILE A1139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  ILE A1137 "
            pdb=" N   ILE A1137 "
            pdb=" C   ILE A1137 "
            pdb=" CB  ILE A1137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 674 not shown)

  Planarity restraints: 759
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1122 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO A1123 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A1123 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A1123 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 437 "    0.019 5.00e-02 4.00e+02   2.80e-02 1.25e+00
        pdb=" N   PRO A 438 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 438 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 438 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1201 "   -0.005 2.00e-02 2.50e+03   1.05e-02 1.09e+00
        pdb=" C   MET A1201 "    0.018 2.00e-02 2.50e+03
        pdb=" O   MET A1201 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP A1202 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 756 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1443
        2.84 -     3.36: 4332
        3.36 -     3.87: 7300
        3.87 -     4.39: 8453
        4.39 -     4.90: 13879
  Nonbonded interactions: 35407
  Sorted by model distance:
  nonbonded pdb=" O   MET A1201 "
            pdb=" N   ILE A1203 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" N   GLU A1098 "
            pdb=" OE1 GLU A1098 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NZ  LYS A 434 "
            pdb=" C2  CLR A1301 "
     model   vdw
     2.353 3.520
  nonbonded pdb=" O   ARG A1204 "
            pdb=" ND2 ASN A 450 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" O   GLU A1056 "
            pdb=" OG  SER A1059 "
     model   vdw
     2.420 3.040
  ... (remaining 35402 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:             1.300
  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:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.950
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4501  Z= 0.227
  Angle     :  0.581   6.930   6096  Z= 0.314
  Chirality :  0.040   0.223    677
  Planarity :  0.003   0.031    759
  Dihedral  : 10.103  85.704   1653
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  2.74 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.36), residues: 547
  helix:  1.91 (0.28), residues: 317
  sheet:  1.64 (0.82), residues: 29
  loop :  0.24 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1007 
 HIS   0.003   0.001   HIS A 231 
 PHE   0.015   0.001   PHE A1124 
 TYR   0.008   0.001   TYR A 398 
 ARG   0.003   0.000   ARG A1106 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TYR cc_start: 0.8547 (t80) cc_final: 0.8130 (t80)
REVERT: A  261 ARG cc_start: 0.8833 (mtt90) cc_final: 0.8621 (ttm110)
REVERT: A  309 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8525 (mp0)
REVERT: A  348 LYS cc_start: 0.8892 (mttt) cc_final: 0.8629 (mtmt)
REVERT: A  384 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8309 (mm-40)
REVERT: A  390 VAL cc_start: 0.9414 (t) cc_final: 0.9178 (p)
REVERT: A 1003 ASP cc_start: 0.6208 (t0) cc_final: 0.5898 (t0)
REVERT: A 1090 HIS cc_start: 0.8396 (m-70) cc_final: 0.7930 (m-70)
REVERT: A 1122 GLU cc_start: 0.7933 (tp30) cc_final: 0.6643 (tp30)
REVERT: A 1123 PRO cc_start: 0.9172 (Cg_exo) cc_final: 0.8716 (Cg_endo)
REVERT: A 1130 GLU cc_start: 0.4917 (tt0) cc_final: 0.4673 (tt0)
REVERT: A 1132 MET cc_start: 0.9281 (mtp) cc_final: 0.8960 (mtp)
REVERT: A 1137 ILE cc_start: 0.8615 (mt) cc_final: 0.8033 (mm)
REVERT: A 1154 THR cc_start: 0.9239 (m) cc_final: 0.8876 (p)
REVERT: A  523 LYS cc_start: 0.9276 (mttt) cc_final: 0.9017 (mttt)
REVERT: A  530 PHE cc_start: 0.9295 (m-80) cc_final: 0.9062 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1737
  time to fit residues: 49.8181
Evaluate side-chains
  152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 288 GLN
A 344 HIS
A1065 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.114043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.095211 restraints weight = 9989.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.098498 restraints weight = 4918.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.100884 restraints weight = 3022.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4501  Z= 0.206
  Angle     :  0.619   8.680   6096  Z= 0.324
  Chirality :  0.043   0.147    677
  Planarity :  0.004   0.026    759
  Dihedral  :  5.195  29.233    663
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.95 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.35), residues: 547
  helix:  2.33 (0.27), residues: 314
  sheet:  2.03 (1.03), residues: 19
  loop : -0.01 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 343 
 HIS   0.006   0.001   HIS A 344 
 PHE   0.019   0.002   PHE A 322 
 TYR   0.012   0.001   TYR A 363 
 ARG   0.005   0.001   ARG A1102 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9298 (mp) cc_final: 0.9075 (mp)
REVERT: A  309 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8609 (mp0)
REVERT: A  348 LYS cc_start: 0.9050 (mttt) cc_final: 0.8792 (mtmt)
REVERT: A 1003 ASP cc_start: 0.6604 (t0) cc_final: 0.5846 (t0)
REVERT: A 1041 PHE cc_start: 0.7466 (m-10) cc_final: 0.7051 (m-10)
REVERT: A 1056 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: A 1090 HIS cc_start: 0.8194 (m-70) cc_final: 0.7883 (m-70)
REVERT: A 1123 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8687 (Cg_endo)
REVERT: A 1154 THR cc_start: 0.9232 (m) cc_final: 0.8913 (p)
REVERT: A  484 TRP cc_start: 0.9069 (m-10) cc_final: 0.8511 (m-90)
REVERT: A  530 PHE cc_start: 0.9395 (m-80) cc_final: 0.9136 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 174
  average time/residue: 0.1866
  time to fit residues: 42.0870
Evaluate side-chains
  158 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  472 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 33 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
A 481 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.110117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.089707 restraints weight = 10216.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.092816 restraints weight = 4983.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.095008 restraints weight = 3083.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4501  Z= 0.262
  Angle     :  0.616   7.108   6096  Z= 0.324
  Chirality :  0.044   0.153    677
  Planarity :  0.004   0.040    759
  Dihedral  :  5.141  26.366    663
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 18.10 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.35), residues: 547
  helix:  2.36 (0.27), residues: 314
  sheet:  1.96 (1.06), residues: 19
  loop : -0.32 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 541 
 HIS   0.001   0.001   HIS A 365 
 PHE   0.015   0.002   PHE A 322 
 TYR   0.015   0.002   TYR A 491 
 ARG   0.008   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8503 (tp30) cc_final: 0.8128 (tm-30)
REVERT: A  232 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8672 (mm-40)
REVERT: A  253 LEU cc_start: 0.9361 (mp) cc_final: 0.9140 (mp)
REVERT: A  309 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8565 (mp0)
REVERT: A  348 LYS cc_start: 0.9090 (mttt) cc_final: 0.8885 (mtmt)
REVERT: A  384 GLN cc_start: 0.9035 (tp40) cc_final: 0.8248 (mt0)
REVERT: A  388 ASP cc_start: 0.9053 (t0) cc_final: 0.8737 (t0)
REVERT: A 1041 PHE cc_start: 0.7542 (m-10) cc_final: 0.7302 (m-80)
REVERT: A 1057 ILE cc_start: 0.9177 (mm) cc_final: 0.8953 (mm)
REVERT: A 1090 HIS cc_start: 0.8352 (m-70) cc_final: 0.8033 (m-70)
REVERT: A 1193 MET cc_start: 0.5273 (mmt) cc_final: 0.3973 (mmt)
REVERT: A  481 GLN cc_start: 0.9097 (tt0) cc_final: 0.8773 (tt0)
REVERT: A  484 TRP cc_start: 0.9164 (m-10) cc_final: 0.8356 (m-90)
REVERT: A  487 SER cc_start: 0.9542 (t) cc_final: 0.9207 (p)
  outliers start: 27
  outliers final: 18
  residues processed: 157
  average time/residue: 0.1373
  time to fit residues: 28.0779
Evaluate side-chains
  153 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0060
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1065 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.107320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.086942 restraints weight = 10515.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.089921 restraints weight = 5145.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.092045 restraints weight = 3196.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4501  Z= 0.321
  Angle     :  0.662  10.033   6096  Z= 0.342
  Chirality :  0.044   0.149    677
  Planarity :  0.004   0.039    759
  Dihedral  :  5.231  33.422    663
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 19.40 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.35), residues: 547
  helix:  2.24 (0.28), residues: 315
  sheet: -0.96 (0.98), residues: 28
  loop : -0.50 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 474 
 PHE   0.013   0.002   PHE A 278 
 TYR   0.013   0.002   TYR A 237 
 ARG   0.010   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9372 (mp) cc_final: 0.9130 (mp)
REVERT: A  309 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8545 (mp0)
REVERT: A  441 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6443 (mp)
REVERT: A 1058 LEU cc_start: 0.9562 (tp) cc_final: 0.9318 (tt)
REVERT: A 1067 MET cc_start: 0.8685 (mpp) cc_final: 0.8470 (pmm)
REVERT: A 1090 HIS cc_start: 0.8409 (m-70) cc_final: 0.8071 (m-70)
REVERT: A 1113 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7720 (p0)
REVERT: A 1124 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7228 (p90)
REVERT: A 1130 GLU cc_start: 0.3834 (tt0) cc_final: 0.3318 (tt0)
REVERT: A 1132 MET cc_start: 0.9369 (mtp) cc_final: 0.8974 (mmm)
REVERT: A 1154 THR cc_start: 0.9336 (m) cc_final: 0.9020 (p)
REVERT: A 1193 MET cc_start: 0.5048 (mmt) cc_final: 0.3243 (mmt)
REVERT: A  487 SER cc_start: 0.9562 (t) cc_final: 0.9226 (p)
  outliers start: 29
  outliers final: 21
  residues processed: 149
  average time/residue: 0.1347
  time to fit residues: 26.3174
Evaluate side-chains
  140 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.110157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.089705 restraints weight = 10443.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.092830 restraints weight = 5083.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.095052 restraints weight = 3120.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4501  Z= 0.204
  Angle     :  0.603   9.176   6096  Z= 0.305
  Chirality :  0.042   0.146    677
  Planarity :  0.004   0.040    759
  Dihedral  :  5.063  37.406    663
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 21.98 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.35), residues: 547
  helix:  2.41 (0.28), residues: 315
  sheet:  0.72 (1.24), residues: 18
  loop : -0.58 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 484 
 HIS   0.001   0.000   HIS A 474 
 PHE   0.015   0.001   PHE A1114 
 TYR   0.011   0.001   TYR A 491 
 ARG   0.011   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 GLN cc_start: 0.8841 (pt0) cc_final: 0.8074 (tm-30)
REVERT: A  253 LEU cc_start: 0.9338 (mp) cc_final: 0.9138 (mp)
REVERT: A  273 TYR cc_start: 0.8879 (m-80) cc_final: 0.8596 (m-10)
REVERT: A  309 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8561 (mp0)
REVERT: A 1058 LEU cc_start: 0.9564 (tp) cc_final: 0.9307 (tt)
REVERT: A 1090 HIS cc_start: 0.8397 (m-70) cc_final: 0.8047 (m-70)
REVERT: A 1113 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7588 (p0)
REVERT: A 1124 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7110 (p90)
REVERT: A 1130 GLU cc_start: 0.3680 (tt0) cc_final: 0.3230 (tt0)
REVERT: A 1132 MET cc_start: 0.9381 (mtp) cc_final: 0.9000 (mmm)
REVERT: A 1148 ASP cc_start: 0.9095 (m-30) cc_final: 0.8858 (m-30)
REVERT: A 1154 THR cc_start: 0.9321 (m) cc_final: 0.8960 (p)
REVERT: A 1193 MET cc_start: 0.4834 (mmt) cc_final: 0.3119 (mmt)
REVERT: A  481 GLN cc_start: 0.9044 (tt0) cc_final: 0.8837 (tt0)
REVERT: A  487 SER cc_start: 0.9522 (t) cc_final: 0.9136 (p)
  outliers start: 23
  outliers final: 17
  residues processed: 144
  average time/residue: 0.1344
  time to fit residues: 25.7454
Evaluate side-chains
  148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.112279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.091799 restraints weight = 10267.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.094963 restraints weight = 5054.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.097141 restraints weight = 3114.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.5193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   4501  Z= 0.209
  Angle     :  0.642  12.429   6096  Z= 0.318
  Chirality :  0.044   0.183    677
  Planarity :  0.004   0.040    759
  Dihedral  :  4.958  38.538    663
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.66 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 21.77 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.35), residues: 547
  helix:  2.56 (0.28), residues: 315
  sheet:  0.62 (1.26), residues: 18
  loop : -0.61 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 484 
 HIS   0.001   0.000   HIS A 474 
 PHE   0.013   0.001   PHE A 373 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.012   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9376 (mp) cc_final: 0.9144 (mp)
REVERT: A  309 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8549 (mp0)
REVERT: A 1040 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6713 (tpt-90)
REVERT: A 1058 LEU cc_start: 0.9531 (tp) cc_final: 0.9129 (tt)
REVERT: A 1090 HIS cc_start: 0.8295 (m-70) cc_final: 0.7954 (m-70)
REVERT: A 1113 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7671 (p0)
REVERT: A 1124 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7082 (p90)
REVERT: A 1130 GLU cc_start: 0.4087 (tt0) cc_final: 0.3610 (tt0)
REVERT: A 1154 THR cc_start: 0.9334 (m) cc_final: 0.9063 (p)
REVERT: A 1193 MET cc_start: 0.4665 (mmt) cc_final: 0.3557 (mmt)
REVERT: A  481 GLN cc_start: 0.9018 (tt0) cc_final: 0.8768 (tt0)
REVERT: A  484 TRP cc_start: 0.9133 (m-10) cc_final: 0.8269 (m-10)
REVERT: A  487 SER cc_start: 0.9504 (t) cc_final: 0.9094 (p)
  outliers start: 26
  outliers final: 18
  residues processed: 146
  average time/residue: 0.1497
  time to fit residues: 28.4420
Evaluate side-chains
  145 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    0.1980
   chunk 29 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
** A 275 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 = 0.3637 r_free = 0.3637 target = 0.117984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.098845 restraints weight = 10219.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.101951 restraints weight = 5077.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.104510 restraints weight = 3175.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.5484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4501  Z= 0.169
  Angle     :  0.633  12.513   6096  Z= 0.313
  Chirality :  0.043   0.210    677
  Planarity :  0.004   0.042    759
  Dihedral  :  4.906  39.698    663
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 25.22 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.36), residues: 547
  helix:  2.48 (0.28), residues: 321
  sheet:  0.45 (1.24), residues: 18
  loop : -0.79 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 539 
 HIS   0.001   0.000   HIS A 365 
 PHE   0.016   0.001   PHE A 373 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.013   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8527 (mp0)
REVERT: A 1002 ILE cc_start: 0.8633 (mm) cc_final: 0.8260 (mm)
REVERT: A 1040 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6731 (tpt-90)
REVERT: A 1058 LEU cc_start: 0.9489 (tp) cc_final: 0.9094 (tt)
REVERT: A 1090 HIS cc_start: 0.8242 (m-70) cc_final: 0.7883 (m-70)
REVERT: A 1124 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7129 (p90)
REVERT: A 1154 THR cc_start: 0.9312 (m) cc_final: 0.9060 (p)
REVERT: A 1193 MET cc_start: 0.4927 (mmt) cc_final: 0.3340 (mmt)
REVERT: A  481 GLN cc_start: 0.9050 (tt0) cc_final: 0.8841 (tt0)
REVERT: A  484 TRP cc_start: 0.9128 (m-10) cc_final: 0.8284 (m-10)
REVERT: A  487 SER cc_start: 0.9486 (t) cc_final: 0.9066 (p)
REVERT: A  541 TRP cc_start: 0.9067 (m-10) cc_final: 0.8639 (m100)
  outliers start: 21
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1446
  time to fit residues: 27.4071
Evaluate side-chains
  146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1065 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.113572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.092812 restraints weight = 10073.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.095796 restraints weight = 5024.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098272 restraints weight = 3207.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.5581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4501  Z= 0.211
  Angle     :  0.668  11.517   6096  Z= 0.329
  Chirality :  0.044   0.222    677
  Planarity :  0.004   0.037    759
  Dihedral  :  4.889  37.603    663
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 24.57 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.36), residues: 547
  helix:  2.57 (0.28), residues: 315
  sheet:  0.43 (1.24), residues: 18
  loop : -0.63 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 539 
 HIS   0.002   0.000   HIS A 365 
 PHE   0.019   0.001   PHE A 373 
 TYR   0.019   0.002   TYR A 273 
 ARG   0.015   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: A 1002 ILE cc_start: 0.8584 (mm) cc_final: 0.8352 (mm)
REVERT: A 1040 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6689 (tpt-90)
REVERT: A 1058 LEU cc_start: 0.9492 (tp) cc_final: 0.9087 (tt)
REVERT: A 1090 HIS cc_start: 0.8355 (m-70) cc_final: 0.7991 (m-70)
REVERT: A 1122 GLU cc_start: 0.6573 (tm-30) cc_final: 0.6371 (tm-30)
REVERT: A 1124 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6930 (p90)
REVERT: A 1130 GLU cc_start: 0.4016 (tt0) cc_final: 0.3444 (tt0)
REVERT: A 1148 ASP cc_start: 0.9067 (m-30) cc_final: 0.8788 (m-30)
REVERT: A 1154 THR cc_start: 0.9270 (m) cc_final: 0.9000 (p)
REVERT: A 1193 MET cc_start: 0.5108 (mmt) cc_final: 0.3909 (mmt)
REVERT: A  481 GLN cc_start: 0.9048 (tt0) cc_final: 0.8804 (tt0)
REVERT: A  484 TRP cc_start: 0.9164 (m-10) cc_final: 0.8249 (m-10)
REVERT: A  487 SER cc_start: 0.9493 (t) cc_final: 0.9072 (p)
REVERT: A  541 TRP cc_start: 0.9049 (m-10) cc_final: 0.8649 (m100)
  outliers start: 24
  outliers final: 19
  residues processed: 145
  average time/residue: 0.1531
  time to fit residues: 29.0431
Evaluate side-chains
  148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0000
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.116466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.095910 restraints weight = 10118.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.099273 restraints weight = 4959.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101656 restraints weight = 3024.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.5831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4501  Z= 0.184
  Angle     :  0.706  14.020   6096  Z= 0.337
  Chirality :  0.043   0.212    677
  Planarity :  0.004   0.040    759
  Dihedral  :  4.843  39.362    663
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.00 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.36), residues: 547
  helix:  2.51 (0.28), residues: 315
  sheet:  0.22 (1.23), residues: 18
  loop : -0.53 (0.42), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 549 
 HIS   0.002   0.000   HIS A 365 
 PHE   0.020   0.001   PHE A 373 
 TYR   0.014   0.001   TYR A 273 
 ARG   0.015   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  232 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8784 (mm110)
REVERT: A  309 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: A  388 ASP cc_start: 0.8876 (t0) cc_final: 0.8141 (t70)
REVERT: A 1040 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6734 (tpt-90)
REVERT: A 1052 LEU cc_start: 0.8923 (mt) cc_final: 0.8577 (tt)
REVERT: A 1058 LEU cc_start: 0.9504 (tp) cc_final: 0.9098 (tt)
REVERT: A 1090 HIS cc_start: 0.8346 (m-70) cc_final: 0.7997 (m-70)
REVERT: A 1124 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6936 (p90)
REVERT: A 1154 THR cc_start: 0.9279 (m) cc_final: 0.9022 (p)
REVERT: A  481 GLN cc_start: 0.9119 (tt0) cc_final: 0.8872 (tt0)
REVERT: A  484 TRP cc_start: 0.9132 (m-10) cc_final: 0.8339 (m-10)
REVERT: A  541 TRP cc_start: 0.9026 (m-10) cc_final: 0.8673 (m100)
  outliers start: 22
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1380
  time to fit residues: 26.1763
Evaluate side-chains
  147 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0020
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 44 optimal weight:    0.4980
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.119266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100109 restraints weight = 10203.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.103412 restraints weight = 5181.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.105601 restraints weight = 3203.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.5971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4501  Z= 0.186
  Angle     :  0.734  14.987   6096  Z= 0.349
  Chirality :  0.044   0.157    677
  Planarity :  0.004   0.037    759
  Dihedral  :  4.832  38.915    663
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.51 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.36), residues: 547
  helix:  2.42 (0.28), residues: 315
  sheet: -0.04 (1.30), residues: 18
  loop : -0.48 (0.42), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 549 
 HIS   0.001   0.000   HIS A 365 
 PHE   0.030   0.001   PHE A 373 
 TYR   0.012   0.001   TYR A 273 
 ARG   0.017   0.001   ARG A1178 

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8810 (mm110)
REVERT: A  388 ASP cc_start: 0.8841 (t0) cc_final: 0.8121 (t70)
REVERT: A 1040 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6768 (tpt-90)
REVERT: A 1052 LEU cc_start: 0.8890 (mt) cc_final: 0.8558 (tt)
REVERT: A 1058 LEU cc_start: 0.9485 (tp) cc_final: 0.9076 (tt)
REVERT: A 1090 HIS cc_start: 0.8313 (m-70) cc_final: 0.7943 (m-70)
REVERT: A 1124 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7038 (p90)
REVERT: A 1154 THR cc_start: 0.9323 (m) cc_final: 0.9058 (p)
REVERT: A  481 GLN cc_start: 0.9029 (tt0) cc_final: 0.8763 (tt0)
REVERT: A  484 TRP cc_start: 0.9129 (m-10) cc_final: 0.8406 (m-90)
REVERT: A  541 TRP cc_start: 0.9023 (m-10) cc_final: 0.8638 (m100)
  outliers start: 20
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1399
  time to fit residues: 26.4985
Evaluate side-chains
  147 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    0.4980
   chunk 34 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3625 r_free = 0.3625 target = 0.116834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.096247 restraints weight = 10111.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.099565 restraints weight = 4984.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101671 restraints weight = 3059.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.6062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4501  Z= 0.192
  Angle     :  0.731  14.707   6096  Z= 0.345
  Chirality :  0.044   0.162    677
  Planarity :  0.004   0.039    759
  Dihedral  :  4.796  38.256    663
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 25.43 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.36), residues: 547
  helix:  2.44 (0.28), residues: 315
  sheet: -0.07 (1.34), residues: 18
  loop : -0.40 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 549 
 HIS   0.001   0.000   HIS A 365 
 PHE   0.012   0.001   PHE A 289 
 TYR   0.012   0.001   TYR A 273 
 ARG   0.016   0.001   ARG A1178 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1755.20 seconds
wall clock time: 31 minutes 7.92 seconds (1867.92 seconds total)