Starting phenix.real_space_refine
on Fri May  9 13:18:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zf7_60052/05_2025/8zf7_60052_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zf7_60052/05_2025/8zf7_60052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zf7_60052/05_2025/8zf7_60052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zf7_60052/05_2025/8zf7_60052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zf7_60052/05_2025/8zf7_60052_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zf7_60052/05_2025/8zf7_60052_neut.cif"
  }
  resolution = 3.15
  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=   0.015
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      13      5.16       5
     C    1356      2.51       5
     N     359      2.21       5
     O     348      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2076
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "R"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2076
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 137
          Unresolved non-hydrogen angles: 173
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 71
  Time building chain proxies: 2.04, per 1000 atoms: 0.98
  Number of scatterers: 2076
  At special positions: 0
  Unit cell: (58.3, 61.48, 73.14, 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      13     16.00
     O     348      8.00
     N     359      7.00
     C    1356      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " 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: 0.53
  Conformation dependent library (CDL) restraints added in 585.0 milliseconds
  

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  528

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 1 sheets defined
      82.3% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 18 through 47
      removed outlier: 4.559A  pdb=" N   LEU R  32 " --> pdb=" O   PHE R  28 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 51 through 79
      removed outlier: 4.125A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 121
      removed outlier: 4.008A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 122 through 125
      removed outlier: 3.915A  pdb=" N   PHE R 125 " --> pdb=" O   PRO R 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 122 through 125'
    Processing helix  chain 'R' and resid 129 through 150
      removed outlier: 3.774A  pdb=" N   SER R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 155
      removed outlier: 3.648A  pdb=" N   GLY R 155 " --> pdb=" O   PRO R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 191
      removed outlier: 3.708A  pdb=" N   ALA R 182 " --> pdb=" O   GLY R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 193 through 209
      removed outlier: 3.588A  pdb=" N   LEU R 209 " --> pdb=" O   LEU R 205 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 253
      removed outlier: 3.538A  pdb=" N   VAL R 223 " --> pdb=" O   GLU R 219 " (cutoff:3.500A)
      Proline residue:  R 231  - end of helix
      Proline residue:  R 240  - end of helix
    Processing helix  chain 'R' and resid 265 through 284
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 287 through 295
    Processing helix  chain 'R' and resid 297 through 308
    Processing sheet with id=AA1, first strand: chain 'R' and resid 158 through 159

    168 hydrogen bonds defined for protein.
    498 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 659
        1.34 -     1.46: 533
        1.46 -     1.58: 927
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 2135
  Sorted by residual:
  bond pdb=" N   ASP R  81 "
       pdb=" CA  ASP R  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.042 1.23e-02 6.61e+03 1.16e+01
  bond pdb=" N   GLY R 155 "
       pdb=" CA  GLY R 155 "
    ideal  model  delta    sigma   weight residual
    1.443  1.459 -0.016 8.60e-03 1.35e+04 3.61e+00
  bond pdb=" CA  ASP R  81 "
       pdb=" CB  ASP R  81 "
    ideal  model  delta    sigma   weight residual
    1.541  1.563 -0.022 1.20e-02 6.94e+03 3.38e+00
  bond pdb=" N   ARG R  79 "
       pdb=" CA  ARG R  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.438  0.020 1.12e-02 7.97e+03 3.07e+00
  bond pdb=" C   GLY R  86 "
       pdb=" N   PRO R  87 "
    ideal  model  delta    sigma   weight residual
    1.336  1.317  0.019 1.20e-02 6.94e+03 2.60e+00
  ... (remaining 2130 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 2769
        1.68 -     3.37: 123
        3.37 -     5.05: 18
        5.05 -     6.73: 14
        6.73 -     8.41: 3
  Bond angle restraints: 2927
  Sorted by residual:
  angle pdb=" N   ASP R  81 "
        pdb=" CA  ASP R  81 "
        pdb=" C   ASP R  81 "
      ideal   model   delta    sigma   weight residual
     113.28  121.69   -8.41 1.57e+00 4.06e-01 2.87e+01
  angle pdb=" N   ARG R  80 "
        pdb=" CA  ARG R  80 "
        pdb=" C   ARG R  80 "
      ideal   model   delta    sigma   weight residual
     111.39  117.21   -5.82 1.38e+00 5.25e-01 1.78e+01
  angle pdb=" N   PRO R  71 "
        pdb=" CA  PRO R  71 "
        pdb=" C   PRO R  71 "
      ideal   model   delta    sigma   weight residual
     110.70  115.30   -4.60 1.22e+00 6.72e-01 1.42e+01
  angle pdb=" N   ARG R  79 "
        pdb=" CA  ARG R  79 "
        pdb=" C   ARG R  79 "
      ideal   model   delta    sigma   weight residual
     112.97  109.47    3.50 1.06e+00 8.90e-01 1.09e+01
  angle pdb=" N   VAL R  82 "
        pdb=" CA  VAL R  82 "
        pdb=" C   VAL R  82 "
      ideal   model   delta    sigma   weight residual
     109.55  113.35   -3.80 1.38e+00 5.25e-01 7.58e+00
  ... (remaining 2922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.13: 1093
       14.13 -    28.26: 109
       28.26 -    42.40: 26
       42.40 -    56.53: 4
       56.53 -    70.66: 2
  Dihedral angle restraints: 1234
    sinusoidal: 404
      harmonic: 830
  Sorted by residual:
  dihedral pdb=" N   ASP R  81 "
           pdb=" C   ASP R  81 "
           pdb=" CA  ASP R  81 "
           pdb=" CB  ASP R  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.58  -11.78     0      2.50e+00 1.60e-01 2.22e+01
  dihedral pdb=" CA  LEU R 192 "
           pdb=" C   LEU R 192 "
           pdb=" N   LEU R 193 "
           pdb=" CA  LEU R 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.57   21.43     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  SER R 175 "
           pdb=" C   SER R 175 "
           pdb=" N   GLY R 176 "
           pdb=" CA  GLY R 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.36   20.64     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 1231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 295
       0.084 -    0.168: 34
       0.168 -    0.252: 1
       0.252 -    0.336: 1
       0.336 -    0.419: 1
  Chirality restraints: 332
  Sorted by residual:
  chirality pdb=" CA  ASP R  81 "
            pdb=" N   ASP R  81 "
            pdb=" C   ASP R  81 "
            pdb=" CB  ASP R  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.40e+00
  chirality pdb=" CA  ARG R  80 "
            pdb=" N   ARG R  80 "
            pdb=" C   ARG R  80 "
            pdb=" CB  ARG R  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  HIS R 276 "
            pdb=" N   HIS R 276 "
            pdb=" C   HIS R 276 "
            pdb=" CB  HIS R 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 329 not shown)

  Planarity restraints: 373
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 230 "   -0.061 5.00e-02 4.00e+02   9.11e-02 1.33e+01
        pdb=" N   PRO R 231 "    0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO R 231 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO R 231 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R  86 "   -0.032 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO R  87 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO R  87 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R  87 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 239 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.53e+00
        pdb=" N   PRO R 240 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO R 240 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 240 "    0.022 5.00e-02 4.00e+02
  ... (remaining 370 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 612
        2.82 -     3.34: 2092
        3.34 -     3.86: 3401
        3.86 -     4.38: 3595
        4.38 -     4.90: 6331
  Nonbonded interactions: 16031
  Sorted by model distance:
  nonbonded pdb=" O   GLY R  31 "
            pdb=" N   ASN R  35 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OE1 GLU R 170 "
            pdb=" OH  TYR R 172 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   TYR R 275 "
            pdb=" OG  SER R 278 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" NH1 ARG R  91 "
            pdb=" O   LEU R 153 "
     model   vdw
     2.496 3.120
  nonbonded pdb=" O   VAL R  18 "
            pdb=" OG  SER R  22 "
     model   vdw
     2.557 3.040
  ... (remaining 16026 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.720
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   2136  Z= 0.297
  Angle     :  0.897   8.413   2929  Z= 0.486
  Chirality :  0.057   0.419    332
  Planarity :  0.008   0.091    373
  Dihedral  : 12.636  70.659    703
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  1.09 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.35 (0.50), residues: 284
  helix:  0.77 (0.36), residues: 218
  sheet:  None (None), residues: 0
  loop : -3.66 (0.57), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R  83 
 HIS   0.009   0.003   HIS R 276 
 PHE   0.015   0.002   PHE R 107 
 TYR   0.016   0.002   TYR R 275 
 ARG   0.008   0.001   ARG R 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13152 (  168)
  hydrogen bonds       : angle       5.52526 (  498)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       1.86924 (    2)
  covalent geometry    : bond        0.00676 ( 2135)
  covalent geometry    : angle       0.89611 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.207 
Fit side-chains
REVERT: R   66 LEU cc_start: 0.8090 (tp) cc_final: 0.7885 (tt)
REVERT: R  236 LEU cc_start: 0.7697 (tp) cc_final: 0.7477 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1618
  time to fit residues: 6.3954
Evaluate side-chains
  31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0970
   chunk 11 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0770
   chunk 14 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0270
   chunk 17 optimal weight:    0.4980
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.1794

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

Flipped N/Q/H residues before XYZ refinement:
R  45 GLN
** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 276 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.125392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.114887 restraints weight = 3250.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.71
r_work: 0.3439 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2136  Z= 0.154
  Angle     :  0.688   6.605   2929  Z= 0.349
  Chirality :  0.041   0.136    332
  Planarity :  0.006   0.061    373
  Dihedral  :  4.682  21.294    318
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.78 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.68 (0.51), residues: 284
  helix:  1.55 (0.36), residues: 214
  sheet:  None (None), residues: 0
  loop : -3.20 (0.59), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  83 
 HIS   0.003   0.001   HIS R 159 
 PHE   0.010   0.001   PHE R 107 
 TYR   0.012   0.001   TYR R 275 
 ARG   0.002   0.000   ARG R 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  168)
  hydrogen bonds       : angle       4.50316 (  498)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       1.65676 (    2)
  covalent geometry    : bond        0.00374 ( 2135)
  covalent geometry    : angle       0.68680 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.201 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 31
  average time/residue: 0.1549
  time to fit residues: 5.6502
Evaluate side-chains
  31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.2956

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

Flipped N/Q/H residues before XYZ refinement:
R 164 ASN
R 276 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.123615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.113197 restraints weight = 3281.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.71
r_work: 0.3414 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2136  Z= 0.172
  Angle     :  0.693   6.599   2929  Z= 0.348
  Chirality :  0.042   0.133    332
  Planarity :  0.006   0.049    373
  Dihedral  :  4.572  21.057    318
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 15.76 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.94 (0.52), residues: 284
  helix:  1.70 (0.37), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.10 (0.61), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  73 
 HIS   0.002   0.001   HIS R 242 
 PHE   0.012   0.001   PHE R 107 
 TYR   0.012   0.001   TYR R 275 
 ARG   0.008   0.001   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  168)
  hydrogen bonds       : angle       4.39623 (  498)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       1.23013 (    2)
  covalent geometry    : bond        0.00423 ( 2135)
  covalent geometry    : angle       0.69227 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.199 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 33
  average time/residue: 0.1821
  time to fit residues: 6.9119
Evaluate side-chains
  29 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0770
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0870
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    0.1980
   chunk 7 optimal weight:    0.3980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.1916

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

Flipped N/Q/H residues before XYZ refinement:
R 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.126461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.116005 restraints weight = 3239.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.74
r_work: 0.3450 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2136  Z= 0.143
  Angle     :  0.667   7.171   2929  Z= 0.333
  Chirality :  0.041   0.130    332
  Planarity :  0.005   0.049    373
  Dihedral  :  4.331  21.412    318
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 17.39 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.33 (0.52), residues: 284
  helix:  1.99 (0.36), residues: 217
  sheet:  None (None), residues: 0
  loop : -3.08 (0.62), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  83 
 HIS   0.002   0.001   HIS R 159 
 PHE   0.010   0.001   PHE R 107 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.002   0.000   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  168)
  hydrogen bonds       : angle       4.18027 (  498)
  SS BOND              : bond        0.00138 (    1)
  SS BOND              : angle       1.00031 (    2)
  covalent geometry    : bond        0.00346 ( 2135)
  covalent geometry    : angle       0.66638 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.213 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 33
  average time/residue: 0.1525
  time to fit residues: 5.9137
Evaluate side-chains
  31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0470
   chunk 5 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0170
   chunk 21 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 17 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.1094

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

Flipped N/Q/H residues before XYZ refinement:
R 159 HIS
R 164 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.128539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.117595 restraints weight = 3245.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.79
r_work: 0.3491 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2136  Z= 0.128
  Angle     :  0.654   6.861   2929  Z= 0.324
  Chirality :  0.039   0.129    332
  Planarity :  0.005   0.049    373
  Dihedral  :  4.117  21.562    318
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.85 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.60 (0.52), residues: 284
  helix:  2.17 (0.36), residues: 219
  sheet:  None (None), residues: 0
  loop : -3.07 (0.64), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  40 
 HIS   0.002   0.001   HIS R 159 
 PHE   0.009   0.001   PHE R 107 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.011   0.001   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  168)
  hydrogen bonds       : angle       3.94860 (  498)
  SS BOND              : bond        0.00111 (    1)
  SS BOND              : angle       0.90441 (    2)
  covalent geometry    : bond        0.00306 ( 2135)
  covalent geometry    : angle       0.65407 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.218 
Fit side-chains
REVERT: R   78 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6484 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 33
  average time/residue: 0.1548
  time to fit residues: 6.0352
Evaluate side-chains
  31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 4 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.1980
   chunk 21 optimal weight:    0.0470
   chunk 22 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.1980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.1478

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

Flipped N/Q/H residues before XYZ refinement:
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 159 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.127651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.116792 restraints weight = 3206.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.77
r_work: 0.3478 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2136  Z= 0.134
  Angle     :  0.685   9.748   2929  Z= 0.333
  Chirality :  0.040   0.131    332
  Planarity :  0.005   0.049    373
  Dihedral  :  4.144  21.460    318
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.02 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.69 (0.52), residues: 284
  helix:  2.24 (0.36), residues: 219
  sheet:  None (None), residues: 0
  loop : -3.07 (0.64), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  43 
 HIS   0.002   0.001   HIS R 159 
 PHE   0.009   0.001   PHE R 107 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.011   0.000   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  168)
  hydrogen bonds       : angle       3.94791 (  498)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.77716 (    2)
  covalent geometry    : bond        0.00326 ( 2135)
  covalent geometry    : angle       0.68530 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.220 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1579
  time to fit residues: 5.6125
Evaluate side-chains
  28 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0870
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0970
   chunk 13 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.2356

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

Flipped N/Q/H residues before XYZ refinement:
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 159 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.125357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.114553 restraints weight = 3257.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.77
r_work: 0.3442 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2136  Z= 0.152
  Angle     :  0.696   8.680   2929  Z= 0.342
  Chirality :  0.041   0.141    332
  Planarity :  0.006   0.055    373
  Dihedral  :  4.252  21.320    318
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 18.48 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.69 (0.52), residues: 284
  helix:  2.23 (0.36), residues: 219
  sheet:  None (None), residues: 0
  loop : -3.04 (0.66), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  43 
 HIS   0.002   0.001   HIS R 242 
 PHE   0.011   0.001   PHE R 107 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.012   0.001   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  168)
  hydrogen bonds       : angle       4.04819 (  498)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.78986 (    2)
  covalent geometry    : bond        0.00379 ( 2135)
  covalent geometry    : angle       0.69602 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.215 
Fit side-chains
REVERT: R   78 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6814 (tp)
REVERT: R  284 LEU cc_start: 0.8087 (tt) cc_final: 0.7746 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1527
  time to fit residues: 5.7416
Evaluate side-chains
  28 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0570
   chunk 26 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0970
   chunk 5 optimal weight:    0.0970
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.2294

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

Flipped N/Q/H residues before XYZ refinement:
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 159 HIS
R 164 ASN
** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.125112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.114354 restraints weight = 3316.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.78
r_work: 0.3439 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2136  Z= 0.154
  Angle     :  0.699   8.399   2929  Z= 0.344
  Chirality :  0.041   0.139    332
  Planarity :  0.005   0.048    373
  Dihedral  :  4.280  21.288    318
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.39 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.62 (0.52), residues: 284
  helix:  2.18 (0.35), residues: 219
  sheet:  None (None), residues: 0
  loop : -3.09 (0.66), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  73 
 HIS   0.002   0.001   HIS R 159 
 PHE   0.011   0.001   PHE R 107 
 TYR   0.012   0.001   TYR R  76 
 ARG   0.007   0.000   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  168)
  hydrogen bonds       : angle       4.08136 (  498)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.75760 (    2)
  covalent geometry    : bond        0.00380 ( 2135)
  covalent geometry    : angle       0.69880 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.201 
Fit side-chains
REVERT: R   78 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6823 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1600
  time to fit residues: 5.8243
Evaluate side-chains
  28 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 6 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    0.1980
   chunk 10 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0980
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    0.1980
   chunk 22 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0770
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.1538

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

Flipped N/Q/H residues before XYZ refinement:
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 159 HIS
R 164 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.116164 restraints weight = 3334.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.79
r_work: 0.3467 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2136  Z= 0.138
  Angle     :  0.682   8.104   2929  Z= 0.337
  Chirality :  0.040   0.163    332
  Planarity :  0.005   0.048    373
  Dihedral  :  4.215  21.442    318
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 19.02 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.66 (0.51), residues: 284
  helix:  2.20 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -3.08 (0.66), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  43 
 HIS   0.002   0.001   HIS R 159 
 PHE   0.011   0.001   PHE R 107 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.002   0.000   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  168)
  hydrogen bonds       : angle       4.00804 (  498)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.63006 (    2)
  covalent geometry    : bond        0.00339 ( 2135)
  covalent geometry    : angle       0.68185 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.199 
Fit side-chains
REVERT: R   78 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6824 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 33
  average time/residue: 0.1601
  time to fit residues: 6.2477
Evaluate side-chains
  33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  169 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 9 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 3 optimal weight:    0.0000
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.1160

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

Flipped N/Q/H residues before XYZ refinement:
R  58 ASN
R 159 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.128186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.117465 restraints weight = 3267.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.78
r_work: 0.3490 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2136  Z= 0.133
  Angle     :  0.680   8.010   2929  Z= 0.335
  Chirality :  0.040   0.151    332
  Planarity :  0.006   0.059    373
  Dihedral  :  4.151  21.256    318
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 20.11 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.80 (0.51), residues: 284
  helix:  2.30 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -3.03 (0.65), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  43 
 HIS   0.002   0.000   HIS R 159 
 PHE   0.010   0.001   PHE R 107 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.013   0.001   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03079 (  168)
  hydrogen bonds       : angle       3.87637 (  498)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.47947 (    2)
  covalent geometry    : bond        0.00329 ( 2135)
  covalent geometry    : angle       0.68006 ( 2927)

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

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

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  568 Ramachandran restraints generated.
    284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.220 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 31
  average time/residue: 0.1661
  time to fit residues: 6.0456
Evaluate side-chains
  31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  169 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 23 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
R 159 HIS
R 276 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.121617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.111423 restraints weight = 3253.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.71
r_work: 0.3392 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   2136  Z= 0.211
  Angle     :  0.748   7.636   2929  Z= 0.374
  Chirality :  0.044   0.153    332
  Planarity :  0.006   0.047    373
  Dihedral  :  4.648  22.123    318
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.11 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.40 (0.51), residues: 284
  helix:  2.06 (0.35), residues: 218
  sheet:  None (None), residues: 0
  loop : -3.19 (0.63), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP R  73 
 HIS   0.002   0.001   HIS R 165 
 PHE   0.011   0.002   PHE R 107 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.007   0.001   ARG R 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04316 (  168)
  hydrogen bonds       : angle       4.33010 (  498)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.62827 (    2)
  covalent geometry    : bond        0.00532 ( 2135)
  covalent geometry    : angle       0.74785 ( 2927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1615.77 seconds
wall clock time: 28 minutes 51.74 seconds (1731.74 seconds total)