Starting phenix.real_space_refine
on Tue Feb 11 12:55:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0b_36759/02_2025/8k0b_36759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0b_36759/02_2025/8k0b_36759.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0b_36759/02_2025/8k0b_36759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0b_36759/02_2025/8k0b_36759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0b_36759/02_2025/8k0b_36759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0b_36759/02_2025/8k0b_36759.cif"
  }
  resolution = 3.56
  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=   0.001 sd=   0.020
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      34      5.16       5
     C    3758      2.51       5
     N     945      2.21       5
     O     952      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5689
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 689, 5689
          Classifications: {'peptide': 689}
          Link IDs: {'PTRANS': 25, 'TRANS': 663}
  Time building chain proxies: 3.95, per 1000 atoms: 0.69
  Number of scatterers: 5689
  At special positions: 0
  Unit cell: (104.94, 93.28, 92.22, 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      34     16.00
     O     952      8.00
     N     945      7.00
     C    3758      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 298 " - pdb=" SG  CYS A 300 " 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: 1.49
  Conformation dependent library (CDL) restraints added in 687.7 milliseconds
  

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1324

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      64.4% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 61
    Processing helix  chain 'A' and resid 63 through 73
      removed outlier: 4.353A  pdb=" N   ALA A  68 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   LEU A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 79
      removed outlier: 3.619A  pdb=" N   LEU A  79 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 98
      removed outlier: 3.959A  pdb=" N   ALA A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 146
      removed outlier: 3.653A  pdb=" N   ARG A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE A 140 " --> pdb=" O   HIS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 151
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 182 through 206
    Processing helix  chain 'A' and resid 231 through 243
      removed outlier: 4.030A  pdb=" N   ILE A 235 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 285
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.944A  pdb=" N   ARG A 296 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 334
      removed outlier: 4.135A  pdb=" N   GLN A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 359
      removed outlier: 3.725A  pdb=" N   VAL A 351 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 364
    Processing helix  chain 'A' and resid 372 through 377
    Processing helix  chain 'A' and resid 406 through 429
      Proline residue:  A 425  - end of helix
    Processing helix  chain 'A' and resid 446 through 477
      removed outlier: 4.132A  pdb=" N   PHE A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      Proline residue:  A 454  - end of helix
      Proline residue:  A 466  - end of helix
    Processing helix  chain 'A' and resid 480 through 502
      removed outlier: 3.968A  pdb=" N   TYR A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 540 through 560
      removed outlier: 4.238A  pdb=" N   ILE A 544 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 574
      removed outlier: 3.833A  pdb=" N   CYS A 566 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 587
      removed outlier: 3.777A  pdb=" N   VAL A 582 " --> pdb=" O   GLU A 578 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN A 587 " --> pdb=" O   HIS A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 612
    Processing helix  chain 'A' and resid 617 through 640
      removed outlier: 3.938A  pdb=" N   PHE A 621 " --> pdb=" O   ILE A 617 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A 635 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 661
      removed outlier: 3.950A  pdb=" N   HIS A 651 " --> pdb=" O   ASN A 647 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR A 656 " --> pdb=" O   MET A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 677
      removed outlier: 3.856A  pdb=" N   GLY A 665 " --> pdb=" O   ALA A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 712
      removed outlier: 3.696A  pdb=" N   LEU A 685 " --> pdb=" O   HIS A 681 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE A 686 " --> pdb=" O   SER A 682 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE A 692 " --> pdb=" O   MET A 688 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 255
      removed outlier: 5.716A  pdb=" N   LEU A 340 " --> pdb=" O   CYS A 254 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR A 223 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ARG A 382 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289

    318 hydrogen bonds defined for protein.
    939 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: 1.59

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 832
        1.31 -     1.44: 1783
        1.44 -     1.56: 3192
        1.56 -     1.69: 0
        1.69 -     1.82: 51
  Bond restraints: 5858
  Sorted by residual:
  bond pdb=" C   TYR A 130 "
       pdb=" O   TYR A 130 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.055 1.15e-02 7.56e+03 2.32e+01
  bond pdb=" CA  TYR A 130 "
       pdb=" C   TYR A 130 "
    ideal  model  delta    sigma   weight residual
    1.524  1.479  0.045 1.24e-02 6.50e+03 1.32e+01
  bond pdb=" CA  SER A 687 "
       pdb=" CB  SER A 687 "
    ideal  model  delta    sigma   weight residual
    1.530  1.478  0.051 1.56e-02 4.11e+03 1.08e+01
  bond pdb=" N   TYR A  54 "
       pdb=" CA  TYR A  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.19e-02 7.06e+03 6.82e+00
  bond pdb=" N   SER A 689 "
       pdb=" CA  SER A 689 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.20e-02 6.94e+03 6.10e+00
  ... (remaining 5853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 7860
        3.25 -     6.51: 82
        6.51 -     9.76: 14
        9.76 -    13.01: 3
       13.01 -    16.27: 2
  Bond angle restraints: 7961
  Sorted by residual:
  angle pdb=" C   TYR A 130 "
        pdb=" CA  TYR A 130 "
        pdb=" CB  TYR A 130 "
      ideal   model   delta    sigma   weight residual
     110.96   94.69   16.27 1.54e+00 4.22e-01 1.12e+02
  angle pdb=" N   HIS A 136 "
        pdb=" CA  HIS A 136 "
        pdb=" C   HIS A 136 "
      ideal   model   delta    sigma   weight residual
     112.87  102.31   10.56 1.20e+00 6.94e-01 7.74e+01
  angle pdb=" N   SER A 687 "
        pdb=" CA  SER A 687 "
        pdb=" C   SER A 687 "
      ideal   model   delta    sigma   weight residual
     111.11  101.72    9.39 1.20e+00 6.94e-01 6.12e+01
  angle pdb=" C   ILE A 131 "
        pdb=" N   THR A 132 "
        pdb=" CA  THR A 132 "
      ideal   model   delta    sigma   weight residual
     120.79  111.26    9.53 1.39e+00 5.18e-01 4.70e+01
  angle pdb=" C   HIS A 136 "
        pdb=" CA  HIS A 136 "
        pdb=" CB  HIS A 136 "
      ideal   model   delta    sigma   weight residual
     110.21  124.85  -14.64 2.19e+00 2.09e-01 4.47e+01
  ... (remaining 7956 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 2883
       17.46 -    34.91: 389
       34.91 -    52.37: 104
       52.37 -    69.83: 22
       69.83 -    87.29: 9
  Dihedral angle restraints: 3407
    sinusoidal: 1361
      harmonic: 2046
  Sorted by residual:
  dihedral pdb=" C   TYR A 130 "
           pdb=" N   TYR A 130 "
           pdb=" CA  TYR A 130 "
           pdb=" CB  TYR A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -103.89  -18.71     0      2.50e+00 1.60e-01 5.60e+01
  dihedral pdb=" CA  LEU A 536 "
           pdb=" C   LEU A 536 "
           pdb=" N   PRO A 537 "
           pdb=" CA  PRO A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.47   32.53     0      5.00e+00 4.00e-02 4.23e+01
  dihedral pdb=" CB  CYS A 298 "
           pdb=" SG  CYS A 298 "
           pdb=" SG  CYS A 300 "
           pdb=" CB  CYS A 300 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.30  -52.30     1      1.00e+01 1.00e-02 3.73e+01
  ... (remaining 3404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 737
       0.057 -    0.114: 139
       0.114 -    0.171: 11
       0.171 -    0.228: 7
       0.228 -    0.286: 2
  Chirality restraints: 896
  Sorted by residual:
  chirality pdb=" CA  TYR A 130 "
            pdb=" N   TYR A 130 "
            pdb=" C   TYR A 130 "
            pdb=" CB  TYR A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  HIS A 136 "
            pdb=" N   HIS A 136 "
            pdb=" C   HIS A 136 "
            pdb=" CB  HIS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  GLN A 134 "
            pdb=" N   GLN A 134 "
            pdb=" C   GLN A 134 "
            pdb=" CB  GLN A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 893 not shown)

  Planarity restraints: 974
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 128 "    0.020 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   ARG A 128 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ARG A 128 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE A 129 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 671 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.94e+00
        pdb=" C   PHE A 671 "    0.055 2.00e-02 2.50e+03
        pdb=" O   PHE A 671 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE A 672 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 193 "   -0.031 2.00e-02 2.50e+03   2.11e-02 8.87e+00
        pdb=" CG  TYR A 193 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 193 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 193 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 193 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 193 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 193 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 193 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 971 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 439
        2.74 -     3.28: 5992
        3.28 -     3.82: 9520
        3.82 -     4.36: 10716
        4.36 -     4.90: 17742
  Nonbonded interactions: 44409
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 636 "
            pdb=" OG  SER A 640 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ASP A 520 "
            pdb=" NH1 ARG A 530 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" O   PHE A 420 "
            pdb=" OG1 THR A 424 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OD1 ASP A 339 "
            pdb=" NH2 ARG A 400 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" OG1 THR A 278 "
            pdb=" OE2 GLU A 312 "
     model   vdw
     2.338 3.040
  ... (remaining 44404 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:             0.980
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.220
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5290
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5858  Z= 0.239
  Angle     :  0.865  16.268   7961  Z= 0.506
  Chirality :  0.047   0.286    896
  Planarity :  0.005   0.057    974
  Dihedral  : 17.336  87.286   2080
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 31.31 %
    Favored  : 67.41 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.63 (0.33), residues: 687
  helix:  0.59 (0.27), residues: 398
  sheet:  0.92 (1.28), residues: 17
  loop : -2.07 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.022   0.001   PHE A 519 
 TYR   0.049   0.002   TYR A 193 
 ARG   0.003   0.000   ARG A 400 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ILE cc_start: 0.6800 (tt) cc_final: 0.6532 (tp)
REVERT: A  221 MET cc_start: 0.4513 (tmm) cc_final: 0.3930 (ppp)
REVERT: A  671 PHE cc_start: 0.7396 (t80) cc_final: 0.7137 (t80)
REVERT: A  688 MET cc_start: 0.6435 (tpp) cc_final: 0.6142 (tpp)
  outliers start: 8
  outliers final: 2
  residues processed: 108
  average time/residue: 0.1726
  time to fit residues: 24.6961
Evaluate side-chains
  106 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  691 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0060
   chunk 17 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 197 ASN
A 593 GLN
A 630 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.241147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.207569 restraints weight = 10896.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.211352 restraints weight = 5601.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.213820 restraints weight = 3609.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.4642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5332
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5858  Z= 0.194
  Angle     :  0.662  12.636   7961  Z= 0.342
  Chirality :  0.043   0.170    896
  Planarity :  0.004   0.059    974
  Dihedral  :  5.418  55.136    766
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 26.36 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.43 (0.33), residues: 687
  helix:  0.77 (0.27), residues: 404
  sheet:  0.98 (1.33), residues: 17
  loop : -2.07 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 668 
 HIS   0.005   0.001   HIS A 362 
 PHE   0.023   0.001   PHE A 140 
 TYR   0.040   0.002   TYR A 193 
 ARG   0.003   0.000   ARG A 382 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 108
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 MET cc_start: 0.4647 (tmm) cc_final: 0.4325 (ppp)
REVERT: A  411 ILE cc_start: 0.7298 (tp) cc_final: 0.7043 (mt)
REVERT: A  437 VAL cc_start: -0.2327 (OUTLIER) cc_final: -0.3080 (m)
REVERT: A  522 TYR cc_start: 0.1220 (OUTLIER) cc_final: -0.0491 (m-80)
REVERT: A  646 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.3847 (pp)
REVERT: A  688 MET cc_start: 0.5457 (tpp) cc_final: 0.5215 (tpp)
REVERT: A  690 SER cc_start: 0.7830 (t) cc_final: 0.7242 (p)
  outliers start: 42
  outliers final: 23
  residues processed: 141
  average time/residue: 0.1651
  time to fit residues: 31.4148
Evaluate side-chains
  129 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  593 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  703 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 2 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 27 optimal weight:   20.0000
   chunk 9 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0670
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.3118

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

Flipped N/Q/H residues before XYZ refinement:
A 136 HIS
A 197 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.241449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.208090 restraints weight = 10852.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.212006 restraints weight = 5530.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.214446 restraints weight = 3561.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5312
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5858  Z= 0.171
  Angle     :  0.659  15.106   7961  Z= 0.333
  Chirality :  0.042   0.171    896
  Planarity :  0.004   0.060    974
  Dihedral  :  5.060  45.539    766
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 24.60 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.32 (0.34), residues: 687
  helix:  0.87 (0.27), residues: 408
  sheet:  1.03 (1.30), residues: 17
  loop : -2.10 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 136 
 PHE   0.026   0.001   PHE A 140 
 TYR   0.034   0.002   TYR A 193 
 ARG   0.002   0.000   ARG A 170 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 ILE cc_start: 0.7287 (tp) cc_final: 0.7062 (mt)
REVERT: A  437 VAL cc_start: -0.2097 (OUTLIER) cc_final: -0.2822 (m)
REVERT: A  500 VAL cc_start: 0.7054 (p) cc_final: 0.6847 (p)
REVERT: A  536 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6298 (mp)
REVERT: A  565 LEU cc_start: 0.1993 (OUTLIER) cc_final: 0.1610 (mm)
REVERT: A  598 TYR cc_start: 0.7461 (m-80) cc_final: 0.7116 (m-80)
REVERT: A  646 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.3909 (pp)
REVERT: A  690 SER cc_start: 0.7719 (t) cc_final: 0.7102 (p)
  outliers start: 46
  outliers final: 29
  residues processed: 141
  average time/residue: 0.1599
  time to fit residues: 30.5116
Evaluate side-chains
  133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  682 SER
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  713 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 28 optimal weight:    0.0000
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0970
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.241357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.207446 restraints weight = 11131.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.211048 restraints weight = 5707.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.213676 restraints weight = 3748.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5338
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5858  Z= 0.177
  Angle     :  0.656  14.262   7961  Z= 0.331
  Chirality :  0.042   0.170    896
  Planarity :  0.004   0.059    974
  Dihedral  :  4.760  32.975    764
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 26.04 %
    Favored  : 67.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.25 (0.33), residues: 687
  helix:  0.93 (0.27), residues: 407
  sheet:  0.72 (1.22), residues: 17
  loop : -2.03 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 668 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.031   0.001   PHE A 140 
 TYR   0.033   0.001   TYR A 193 
 ARG   0.009   0.000   ARG A 400 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 101
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.5715 (t80) cc_final: 0.5452 (t80)
REVERT: A  406 THR cc_start: 0.7351 (p) cc_final: 0.7149 (t)
REVERT: A  411 ILE cc_start: 0.7283 (tp) cc_final: 0.7060 (mt)
REVERT: A  433 ASP cc_start: 0.4450 (OUTLIER) cc_final: 0.3295 (p0)
REVERT: A  437 VAL cc_start: -0.2397 (OUTLIER) cc_final: -0.3243 (m)
REVERT: A  536 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.5904 (mt)
REVERT: A  565 LEU cc_start: 0.1891 (OUTLIER) cc_final: 0.1690 (mm)
REVERT: A  598 TYR cc_start: 0.7505 (m-80) cc_final: 0.6225 (m-80)
REVERT: A  608 VAL cc_start: 0.7760 (t) cc_final: 0.7558 (p)
REVERT: A  625 TYR cc_start: 0.7298 (t80) cc_final: 0.7080 (t80)
REVERT: A  646 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.4049 (pp)
REVERT: A  685 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6117 (mm)
REVERT: A  688 MET cc_start: 0.5537 (tpp) cc_final: 0.5225 (ttp)
REVERT: A  690 SER cc_start: 0.7662 (t) cc_final: 0.7096 (p)
  outliers start: 41
  outliers final: 26
  residues processed: 133
  average time/residue: 0.1641
  time to fit residues: 29.2096
Evaluate side-chains
  133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain A residue  682 SER
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  703 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0070
   chunk 27 optimal weight:    0.0470
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 ASN
A 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.240866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.206628 restraints weight = 10716.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.210795 restraints weight = 5493.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.213312 restraints weight = 3512.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.4634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5363
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5858  Z= 0.194
  Angle     :  0.666  15.051   7961  Z= 0.337
  Chirality :  0.042   0.172    896
  Planarity :  0.004   0.061    974
  Dihedral  :  4.676  33.148    764
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 25.08 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.25 (0.33), residues: 687
  helix:  0.93 (0.27), residues: 406
  sheet:  0.84 (1.24), residues: 17
  loop : -2.03 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 668 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.029   0.001   PHE A 140 
 TYR   0.035   0.002   TYR A 193 
 ARG   0.006   0.000   ARG A 400 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 104
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.5629 (t80) cc_final: 0.5380 (t80)
REVERT: A  411 ILE cc_start: 0.7307 (tp) cc_final: 0.7101 (mt)
REVERT: A  433 ASP cc_start: 0.4327 (OUTLIER) cc_final: 0.3067 (p0)
REVERT: A  437 VAL cc_start: -0.2447 (OUTLIER) cc_final: -0.3205 (m)
REVERT: A  450 THR cc_start: 0.7435 (m) cc_final: 0.7226 (m)
REVERT: A  522 TYR cc_start: 0.1285 (OUTLIER) cc_final: -0.0364 (m-80)
REVERT: A  536 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.5990 (mt)
REVERT: A  565 LEU cc_start: 0.1884 (OUTLIER) cc_final: 0.1474 (mm)
REVERT: A  598 TYR cc_start: 0.7447 (m-80) cc_final: 0.5970 (m-80)
REVERT: A  608 VAL cc_start: 0.7734 (t) cc_final: 0.7533 (p)
REVERT: A  646 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.4033 (pp)
REVERT: A  685 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6162 (mm)
  outliers start: 50
  outliers final: 29
  residues processed: 140
  average time/residue: 0.1514
  time to fit residues: 28.5736
Evaluate side-chains
  136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain A residue  557 MET
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain A residue  682 SER
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0970
   chunk 40 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0770
   chunk 60 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0970
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   chunk 4 optimal weight:    0.0770
   overall best weight:    0.0850

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

Flipped N/Q/H residues before XYZ refinement:
A 136 HIS
A 197 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.242099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.210056 restraints weight = 10720.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.213774 restraints weight = 5466.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.216215 restraints weight = 3510.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.4667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5244
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5858  Z= 0.155
  Angle     :  0.671  14.434   7961  Z= 0.334
  Chirality :  0.041   0.183    896
  Planarity :  0.004   0.058    974
  Dihedral  :  4.416  32.654    762
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 27.64 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.12 (0.34), residues: 687
  helix:  0.96 (0.27), residues: 413
  sheet:  0.73 (1.21), residues: 17
  loop : -1.92 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 668 
 HIS   0.005   0.000   HIS A 136 
 PHE   0.029   0.001   PHE A 140 
 TYR   0.028   0.001   TYR A 193 
 ARG   0.005   0.000   ARG A 115 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 97
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.5578 (t80) cc_final: 0.5295 (t80)
REVERT: A  275 LEU cc_start: -0.0627 (OUTLIER) cc_final: -0.0834 (mt)
REVERT: A  411 ILE cc_start: 0.7317 (tp) cc_final: 0.7104 (mt)
REVERT: A  433 ASP cc_start: 0.4139 (OUTLIER) cc_final: 0.3155 (p0)
REVERT: A  437 VAL cc_start: -0.2057 (OUTLIER) cc_final: -0.2891 (m)
REVERT: A  500 VAL cc_start: 0.7178 (OUTLIER) cc_final: 0.6909 (t)
REVERT: A  522 TYR cc_start: 0.1427 (OUTLIER) cc_final: -0.0446 (m-80)
REVERT: A  598 TYR cc_start: 0.7446 (m-80) cc_final: 0.5896 (m-80)
REVERT: A  608 VAL cc_start: 0.7817 (t) cc_final: 0.7587 (p)
REVERT: A  646 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.4212 (pp)
REVERT: A  685 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.6034 (mm)
  outliers start: 43
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1669
  time to fit residues: 28.7037
Evaluate side-chains
  127 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  135 TYR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  682 SER
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 12 optimal weight:    0.0050
   chunk 46 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.4594

-------------------------------------------------------------------------------
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 = 0.4902 r_free = 0.4902 target = 0.240832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.207081 restraints weight = 10789.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.211178 restraints weight = 5468.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.213739 restraints weight = 3493.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.4640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5343
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5858  Z= 0.191
  Angle     :  0.683  14.753   7961  Z= 0.345
  Chirality :  0.042   0.162    896
  Planarity :  0.004   0.060    974
  Dihedral  :  4.461  32.864    762
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 27.80 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.27 (0.33), residues: 687
  helix:  0.89 (0.27), residues: 412
  sheet:  0.57 (1.16), residues: 17
  loop : -2.04 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 668 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.030   0.001   PHE A 140 
 TYR   0.057   0.002   TYR A 193 
 ARG   0.007   0.000   ARG A 571 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 100
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.5720 (t80) cc_final: 0.5468 (t80)
REVERT: A  433 ASP cc_start: 0.4236 (OUTLIER) cc_final: 0.2964 (p0)
REVERT: A  437 VAL cc_start: -0.2386 (OUTLIER) cc_final: -0.3143 (m)
REVERT: A  522 TYR cc_start: 0.1099 (OUTLIER) cc_final: -0.0525 (m-80)
REVERT: A  536 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6026 (mt)
REVERT: A  598 TYR cc_start: 0.7448 (m-80) cc_final: 0.5876 (m-80)
REVERT: A  671 PHE cc_start: 0.7438 (t80) cc_final: 0.7226 (t80)
REVERT: A  685 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6225 (mm)
  outliers start: 42
  outliers final: 28
  residues processed: 133
  average time/residue: 0.1536
  time to fit residues: 27.4204
Evaluate side-chains
  130 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 97
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  135 TYR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  557 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  682 SER
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0010
   chunk 42 optimal weight:    0.0870
   chunk 50 optimal weight:    0.0980
   chunk 66 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   overall best weight:    0.2222

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

Flipped N/Q/H residues before XYZ refinement:
A 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4913 r_free = 0.4913 target = 0.241880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.208264 restraints weight = 10768.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.212327 restraints weight = 5599.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.214637 restraints weight = 3630.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.4657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5307
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5858  Z= 0.164
  Angle     :  0.685  14.612   7961  Z= 0.341
  Chirality :  0.042   0.176    896
  Planarity :  0.004   0.059    974
  Dihedral  :  4.414  32.600    762
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 27.96 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.16 (0.33), residues: 687
  helix:  0.93 (0.26), residues: 413
  sheet:  0.90 (1.21), residues: 17
  loop : -1.94 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 136 
 PHE   0.028   0.001   PHE A 140 
 TYR   0.045   0.002   TYR A 193 
 ARG   0.006   0.000   ARG A 571 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 99
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.5622 (t80) cc_final: 0.5337 (t80)
REVERT: A  433 ASP cc_start: 0.4086 (OUTLIER) cc_final: 0.3060 (p0)
REVERT: A  437 VAL cc_start: -0.2459 (OUTLIER) cc_final: -0.3280 (m)
REVERT: A  500 VAL cc_start: 0.7135 (p) cc_final: 0.6903 (t)
REVERT: A  522 TYR cc_start: 0.1111 (OUTLIER) cc_final: -0.0503 (m-80)
REVERT: A  598 TYR cc_start: 0.7403 (m-80) cc_final: 0.5771 (m-80)
REVERT: A  685 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6153 (mm)
  outliers start: 40
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1771
  time to fit residues: 30.7215
Evaluate side-chains
  128 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  557 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  682 SER
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 136 HIS
A 583 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.239437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.204933 restraints weight = 10657.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.208772 restraints weight = 5497.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.211312 restraints weight = 3575.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5395
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   5858  Z= 0.236
  Angle     :  0.740  14.992   7961  Z= 0.373
  Chirality :  0.044   0.167    896
  Planarity :  0.005   0.060    974
  Dihedral  :  4.578  33.086    762
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 28.75 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.40 (0.33), residues: 687
  helix:  0.70 (0.26), residues: 415
  sheet:  0.84 (1.18), residues: 17
  loop : -1.98 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 479 
 HIS   0.005   0.001   HIS A 362 
 PHE   0.026   0.001   PHE A 140 
 TYR   0.052   0.002   TYR A 193 
 ARG   0.005   0.000   ARG A 571 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 THR cc_start: 0.7737 (t) cc_final: 0.7359 (p)
REVERT: A  433 ASP cc_start: 0.4172 (OUTLIER) cc_final: 0.2839 (p0)
REVERT: A  437 VAL cc_start: -0.2333 (OUTLIER) cc_final: -0.3148 (m)
REVERT: A  522 TYR cc_start: 0.1126 (OUTLIER) cc_final: -0.0681 (m-80)
REVERT: A  536 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.5942 (mt)
REVERT: A  671 PHE cc_start: 0.7692 (t80) cc_final: 0.7480 (t80)
REVERT: A  685 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6235 (mm)
  outliers start: 33
  outliers final: 24
  residues processed: 130
  average time/residue: 0.1636
  time to fit residues: 28.4876
Evaluate side-chains
  129 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  135 TYR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  557 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  583 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    0.0000
   chunk 13 optimal weight:    0.4980
   chunk 22 optimal weight:   20.0000
   chunk 66 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 HIS
A 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.239583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.205546 restraints weight = 10719.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.209454 restraints weight = 5493.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.212044 restraints weight = 3561.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.4628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5378
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5858  Z= 0.212
  Angle     :  0.751  15.399   7961  Z= 0.374
  Chirality :  0.044   0.197    896
  Planarity :  0.005   0.061    974
  Dihedral  :  4.619  33.323    762
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 29.87 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.45 (0.33), residues: 687
  helix:  0.66 (0.26), residues: 414
  sheet:  0.85 (1.18), residues: 17
  loop : -2.00 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 479 
 HIS   0.009   0.001   HIS A 651 
 PHE   0.025   0.001   PHE A 140 
 TYR   0.049   0.002   TYR A 193 
 ARG   0.009   0.000   ARG A 170 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.5521 (t80) cc_final: 0.5308 (t80)
REVERT: A  172 THR cc_start: 0.7759 (t) cc_final: 0.7385 (p)
REVERT: A  433 ASP cc_start: 0.4039 (OUTLIER) cc_final: 0.2780 (p0)
REVERT: A  437 VAL cc_start: -0.2434 (OUTLIER) cc_final: -0.3258 (m)
REVERT: A  522 TYR cc_start: 0.1144 (OUTLIER) cc_final: -0.0433 (m-80)
REVERT: A  536 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.5974 (mt)
REVERT: A  598 TYR cc_start: 0.7339 (m-80) cc_final: 0.5927 (m-80)
REVERT: A  671 PHE cc_start: 0.7708 (t80) cc_final: 0.7454 (t80)
REVERT: A  685 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6209 (mm)
REVERT: A  690 SER cc_start: 0.7728 (t) cc_final: 0.7102 (p)
  outliers start: 28
  outliers final: 23
  residues processed: 122
  average time/residue: 0.1662
  time to fit residues: 27.3731
Evaluate side-chains
  129 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  135 TYR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  404 TRP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  433 ASP
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  557 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 2 optimal weight:    0.0670
   chunk 27 optimal weight:   40.0000
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 22 optimal weight:    7.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 583 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.238884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.204966 restraints weight = 10715.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.208968 restraints weight = 5532.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.211397 restraints weight = 3593.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.4618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5407
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5858  Z= 0.222
  Angle     :  0.764  15.703   7961  Z= 0.382
  Chirality :  0.044   0.193    896
  Planarity :  0.004   0.059    974
  Dihedral  :  4.645  33.265    762
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.07 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -0.54 (0.33), residues: 687
  helix:  0.57 (0.26), residues: 412
  sheet:  0.85 (1.16), residues: 17
  loop : -1.98 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 479 
 HIS   0.008   0.001   HIS A 651 
 PHE   0.024   0.001   PHE A 140 
 TYR   0.049   0.002   TYR A 193 
 ARG   0.009   0.000   ARG A 170 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2186.24 seconds
wall clock time: 40 minutes 0.64 seconds (2400.64 seconds total)