Starting phenix.real_space_refine
on Fri May  9 12:55:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w77_37336/05_2025/8w77_37336_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w77_37336/05_2025/8w77_37336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w77_37336/05_2025/8w77_37336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w77_37336/05_2025/8w77_37336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w77_37336/05_2025/8w77_37336_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w77_37336/05_2025/8w77_37336_neut.cif"
  }
  resolution = 3.61
  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=   0.011
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       4      5.16       5
     C    1043      2.51       5
     N     274      2.21       5
     O     280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 1601
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 1601
          Classifications: {'peptide': 260}
          Incomplete info: {'truncation_to_alanine': 139}
          Link IDs: {'PTRANS': 14, 'TRANS': 245}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 483
          Unresolved non-hydrogen angles: 619
          Unresolved non-hydrogen dihedrals: 399
          Unresolved non-hydrogen chiralities: 70
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 191
  Time building chain proxies: 2.11, per 1000 atoms: 1.32
  Number of scatterers: 1601
  At special positions: 0
  Unit cell: (60.208, 59.36, 75.472, 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       4     16.00
     O     280      8.00
     N     274      7.00
     C    1043      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 181 " 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: 0.44
  Conformation dependent library (CDL) restraints added in 237.7 milliseconds
  

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  498

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 1 sheets defined
      83.5% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 52
      removed outlier: 4.341A  pdb=" N   PHE A  33 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ILE A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 77
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 3.637A  pdb=" N   MET A  83 " --> pdb=" O   THR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 130
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 139 through 159
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 4.117A  pdb=" N   PHE A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 188
      removed outlier: 3.673A  pdb=" N   LYS A 188 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 209
      removed outlier: 3.820A  pdb=" N   TYR A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 226
      removed outlier: 3.635A  pdb=" N   ILE A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
      removed outlier: 3.620A  pdb=" N   THR A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 238 through 242'
    Processing helix  chain 'A' and resid 243 through 264
      removed outlier: 3.641A  pdb=" N   ILE A 247 " --> pdb=" O   CYS A 243 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   CYS A 248 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 271 through 294
      removed outlier: 3.587A  pdb=" N   HIS A 275 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
      Proline residue:  A 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95
      removed outlier: 8.868A  pdb=" N   ILE A 176 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LEU A  15 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)

    142 hydrogen bonds defined for protein.
    426 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: 0.41

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 418
        1.33 -     1.45: 269
        1.45 -     1.57: 944
        1.57 -     1.69: 0
        1.69 -     1.80: 4
  Bond restraints: 1635
  Sorted by residual:
  bond pdb=" N   PRO A  11 "
       pdb=" CD  PRO A  11 "
    ideal  model  delta    sigma   weight residual
    1.473  1.529 -0.056 1.40e-02 5.10e+03 1.59e+01
  bond pdb=" C   MET A 112 "
       pdb=" O   MET A 112 "
    ideal  model  delta    sigma   weight residual
    1.237  1.217  0.019 1.19e-02 7.06e+03 2.66e+00
  bond pdb=" C   MET A 112 "
       pdb=" N   GLU A 113 "
    ideal  model  delta    sigma   weight residual
    1.335  1.316  0.019 1.31e-02 5.83e+03 2.00e+00
  bond pdb=" C   LEU A 156 "
       pdb=" O   LEU A 156 "
    ideal  model  delta    sigma   weight residual
    1.237  1.220  0.016 1.17e-02 7.31e+03 1.94e+00
  bond pdb=" N   MET A 112 "
       pdb=" CA  MET A 112 "
    ideal  model  delta    sigma   weight residual
    1.459  1.444  0.015 1.23e-02 6.61e+03 1.45e+00
  ... (remaining 1630 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 2179
        1.52 -     3.03: 64
        3.03 -     4.55: 9
        4.55 -     6.06: 8
        6.06 -     7.58: 3
  Bond angle restraints: 2263
  Sorted by residual:
  angle pdb=" N   ILE A 159 "
        pdb=" CA  ILE A 159 "
        pdb=" C   ILE A 159 "
      ideal   model   delta    sigma   weight residual
     108.88  116.46   -7.58 2.16e+00 2.14e-01 1.23e+01
  angle pdb=" CA  PRO A  11 "
        pdb=" N   PRO A  11 "
        pdb=" CD  PRO A  11 "
      ideal   model   delta    sigma   weight residual
     112.00  107.30    4.70 1.40e+00 5.10e-01 1.13e+01
  angle pdb=" N   VAL A 209 "
        pdb=" CA  VAL A 209 "
        pdb=" C   VAL A 209 "
      ideal   model   delta    sigma   weight residual
     112.12  109.39    2.73 8.40e-01 1.42e+00 1.06e+01
  angle pdb=" N   LEU A 138 "
        pdb=" CA  LEU A 138 "
        pdb=" C   LEU A 138 "
      ideal   model   delta    sigma   weight residual
     108.73  104.41    4.32 1.63e+00 3.76e-01 7.03e+00
  angle pdb=" CA  ARG A 225 "
        pdb=" C   ARG A 225 "
        pdb=" N   ALA A 226 "
      ideal   model   delta    sigma   weight residual
     118.14  114.70    3.44 1.31e+00 5.83e-01 6.89e+00
  ... (remaining 2258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.17: 854
        9.17 -    18.35: 46
       18.35 -    27.52: 25
       27.52 -    36.70: 16
       36.70 -    45.87: 3
  Dihedral angle restraints: 944
    sinusoidal: 183
      harmonic: 761
  Sorted by residual:
  dihedral pdb=" CB  CYS A  99 "
           pdb=" SG  CYS A  99 "
           pdb=" SG  CYS A 181 "
           pdb=" CB  CYS A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -118.22   32.22     1      1.00e+01 1.00e-02 1.48e+01
  dihedral pdb=" CA  LEU A 164 "
           pdb=" CB  LEU A 164 "
           pdb=" CG  LEU A 164 "
           pdb=" CD1 LEU A 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.85   42.15     3      1.50e+01 4.44e-03 7.56e+00
  dihedral pdb=" SG  CYS A  99 "
           pdb=" CB  CYS A 181 "
           pdb=" SG  CYS A 181 "
           pdb=" CA  CYS A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     183.00  140.82   42.18     1      2.00e+01 2.50e-03 6.21e+00
  ... (remaining 941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 182
       0.040 -    0.080: 76
       0.080 -    0.120: 22
       0.120 -    0.160: 5
       0.160 -    0.200: 2
  Chirality restraints: 287
  Sorted by residual:
  chirality pdb=" CA  ALA A 226 "
            pdb=" N   ALA A 226 "
            pdb=" C   ALA A 226 "
            pdb=" CB  ALA A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CA  LEU A 237 "
            pdb=" N   LEU A 237 "
            pdb=" C   LEU A 237 "
            pdb=" CB  LEU A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.12e-01
  chirality pdb=" CA  LEU A 138 "
            pdb=" N   LEU A 138 "
            pdb=" C   LEU A 138 "
            pdb=" CB  LEU A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.59e-01
  ... (remaining 284 not shown)

  Planarity restraints: 298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 225 "   -0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   ARG A 225 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ARG A 225 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ALA A 226 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 159 "   -0.040 5.00e-02 4.00e+02   5.95e-02 5.66e+00
        pdb=" N   PRO A 160 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 160 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 160 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 286 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO A 287 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "    0.031 5.00e-02 4.00e+02
  ... (remaining 295 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 734
        2.95 -     3.44: 1732
        3.44 -     3.93: 2396
        3.93 -     4.41: 2364
        4.41 -     4.90: 4134
  Nonbonded interactions: 11360
  Sorted by model distance:
  nonbonded pdb=" O   THR A 135 "
            pdb=" O   LEU A 138 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" ND2 ASN A  44 "
            pdb=" OD2 ASP A  72 "
     model   vdw
     2.505 3.120
  nonbonded pdb=" N   HIS A 178 "
            pdb=" O   HIS A 178 "
     model   vdw
     2.636 2.496
  nonbonded pdb=" O   THR A 139 "
            pdb=" C   ASN A 140 "
     model   vdw
     2.637 3.270
  nonbonded pdb=" N   LEU A  57 "
            pdb=" N   HIS A  58 "
     model   vdw
     2.644 2.560
  ... (remaining 11355 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.720
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
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   0.056   1636  Z= 0.221
  Angle     :  0.706   7.581   2265  Z= 0.416
  Chirality :  0.049   0.200    287
  Planarity :  0.007   0.059    298
  Dihedral  : 10.064  45.872    443
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 0.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.56), residues: 248
  helix:  2.46 (0.39), residues: 189
  sheet:  None (None), residues: 0
  loop : -1.27 (0.80), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 183 
 PHE   0.004   0.001   PHE A 161 
 TYR   0.008   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15369 (  142)
  hydrogen bonds       : angle       6.31674 (  426)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.15888 (    2)
  covalent geometry    : bond        0.00368 ( 1635)
  covalent geometry    : angle       0.70630 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8388 (tp) cc_final: 0.8146 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0500
  time to fit residues: 1.9660
Evaluate side-chains
  20 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0670
   chunk 15 optimal weight:    0.0060
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.5534

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.148922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.135910 restraints weight = 3549.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.137424 restraints weight = 2233.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.138352 restraints weight = 1680.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   1636  Z= 0.125
  Angle     :  0.498   4.984   2265  Z= 0.259
  Chirality :  0.042   0.123    287
  Planarity :  0.006   0.050    298
  Dihedral  :  3.086  11.212    263
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.78 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.34 (0.56), residues: 248
  helix:  2.99 (0.38), residues: 194
  sheet:  None (None), residues: 0
  loop : -0.92 (0.89), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 246 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.009   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04346 (  142)
  hydrogen bonds       : angle       4.29747 (  426)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       0.15062 (    2)
  covalent geometry    : bond        0.00250 ( 1635)
  covalent geometry    : angle       0.49824 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8910 (tp) cc_final: 0.8585 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0435
  time to fit residues: 1.6608
Evaluate side-chains
  23 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0370
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6660

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.145669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132427 restraints weight = 3493.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133859 restraints weight = 2178.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.134992 restraints weight = 1664.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1636  Z= 0.124
  Angle     :  0.494   5.037   2265  Z= 0.254
  Chirality :  0.042   0.123    287
  Planarity :  0.005   0.050    298
  Dihedral  :  3.017  11.268    263
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.67 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.62 (0.56), residues: 248
  helix:  3.25 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.10 (0.85), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 
 PHE   0.007   0.001   PHE A  64 
 TYR   0.011   0.001   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04343 (  142)
  hydrogen bonds       : angle       3.98670 (  426)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.18628 (    2)
  covalent geometry    : bond        0.00269 ( 1635)
  covalent geometry    : angle       0.49463 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8884 (tp) cc_final: 0.8545 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 21
  average time/residue: 0.0398
  time to fit residues: 1.3801
Evaluate side-chains
  21 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0040
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5992

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.145495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.132007 restraints weight = 3498.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.133587 restraints weight = 2183.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.134695 restraints weight = 1622.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   1636  Z= 0.117
  Angle     :  0.486   5.039   2265  Z= 0.246
  Chirality :  0.042   0.123    287
  Planarity :  0.005   0.048    298
  Dihedral  :  2.919  11.480    263
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.56 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.74 (0.56), residues: 248
  helix:  3.35 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.21 (0.85), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.004   0.001   HIS A 246 
 PHE   0.006   0.001   PHE A  64 
 TYR   0.010   0.001   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  142)
  hydrogen bonds       : angle       3.76809 (  426)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.27539 (    2)
  covalent geometry    : bond        0.00250 ( 1635)
  covalent geometry    : angle       0.48621 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8846 (tp) cc_final: 0.8526 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 23
  average time/residue: 0.0454
  time to fit residues: 1.6295
Evaluate side-chains
  23 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0000
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.143675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.130030 restraints weight = 3537.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.131660 restraints weight = 2203.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132819 restraints weight = 1624.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1636  Z= 0.126
  Angle     :  0.499   5.076   2265  Z= 0.252
  Chirality :  0.042   0.123    287
  Planarity :  0.005   0.047    298
  Dihedral  :  2.966  11.330    263
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.67 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.79 (0.56), residues: 248
  helix:  3.40 (0.38), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.23 (0.85), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 246 
 PHE   0.005   0.001   PHE A 161 
 TYR   0.011   0.001   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04378 (  142)
  hydrogen bonds       : angle       3.79333 (  426)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       0.19017 (    2)
  covalent geometry    : bond        0.00275 ( 1635)
  covalent geometry    : angle       0.49903 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8861 (tp) cc_final: 0.8521 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 23
  average time/residue: 0.0417
  time to fit residues: 1.5217
Evaluate side-chains
  24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 246 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.142582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.129012 restraints weight = 3582.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.130643 restraints weight = 2271.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.131750 restraints weight = 1669.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1636  Z= 0.145
  Angle     :  0.525   5.182   2265  Z= 0.267
  Chirality :  0.043   0.124    287
  Planarity :  0.005   0.046    298
  Dihedral  :  3.130  12.660    263
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 13.33 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.59 (0.56), residues: 248
  helix:  3.28 (0.38), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.31 (0.84), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.004   0.001   HIS A 246 
 PHE   0.006   0.001   PHE A 161 
 TYR   0.014   0.001   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04901 (  142)
  hydrogen bonds       : angle       3.91664 (  426)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.25917 (    2)
  covalent geometry    : bond        0.00322 ( 1635)
  covalent geometry    : angle       0.52522 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8908 (tp) cc_final: 0.8577 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0431
  time to fit residues: 1.6644
Evaluate side-chains
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  221 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0270
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0030
   overall best weight:    0.4248

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.146193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.132829 restraints weight = 3515.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.134216 restraints weight = 2200.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.135405 restraints weight = 1663.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   1636  Z= 0.110
  Angle     :  0.489   5.623   2265  Z= 0.243
  Chirality :  0.041   0.123    287
  Planarity :  0.005   0.046    298
  Dihedral  :  2.886  10.924    263
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.67 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.90 (0.56), residues: 248
  helix:  3.47 (0.38), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.18 (0.86), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 246 
 PHE   0.003   0.000   PHE A  64 
 TYR   0.007   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  142)
  hydrogen bonds       : angle       3.62523 (  426)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       0.50390 (    2)
  covalent geometry    : bond        0.00224 ( 1635)
  covalent geometry    : angle       0.48939 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8834 (tp) cc_final: 0.8503 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 27
  average time/residue: 0.0427
  time to fit residues: 1.7774
Evaluate side-chains
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.145096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.131682 restraints weight = 3486.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.133368 restraints weight = 2107.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.134507 restraints weight = 1560.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   1636  Z= 0.115
  Angle     :  0.499   5.883   2265  Z= 0.247
  Chirality :  0.042   0.123    287
  Planarity :  0.005   0.046    298
  Dihedral  :  2.894  11.264    263
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.11 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.90 (0.56), residues: 248
  helix:  3.47 (0.38), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.20 (0.86), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 
 PHE   0.004   0.001   PHE A 161 
 TYR   0.009   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  142)
  hydrogen bonds       : angle       3.61777 (  426)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       0.29169 (    2)
  covalent geometry    : bond        0.00245 ( 1635)
  covalent geometry    : angle       0.49920 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8822 (tp) cc_final: 0.8512 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 24
  average time/residue: 0.0435
  time to fit residues: 1.6336
Evaluate side-chains
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 22 optimal weight:    0.0270
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0060
   chunk 2 optimal weight:    0.0570
   chunk 24 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0770
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.1330

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.149811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.136753 restraints weight = 3607.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.138410 restraints weight = 2246.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.139644 restraints weight = 1646.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   1636  Z= 0.099
  Angle     :  0.484   6.902   2265  Z= 0.234
  Chirality :  0.041   0.123    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.696  10.546    263
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.11 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  4.01 (0.56), residues: 248
  helix:  3.32 (0.37), residues: 202
  sheet:  None (None), residues: 0
  loop : -0.75 (0.93), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.001   0.000   HIS A 275 
 PHE   0.005   0.000   PHE A  64 
 TYR   0.006   0.000   TYR A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03093 (  142)
  hydrogen bonds       : angle       3.36273 (  426)
  SS BOND              : bond        0.00340 (    1)
  SS BOND              : angle       0.72629 (    2)
  covalent geometry    : bond        0.00188 ( 1635)
  covalent geometry    : angle       0.48340 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  126 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7348 (p)
REVERT: A  283 LEU cc_start: 0.8753 (tp) cc_final: 0.8471 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 26
  average time/residue: 0.0398
  time to fit residues: 1.6115
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3982 r_free = 0.3982 target = 0.144506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.131041 restraints weight = 3553.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.132743 restraints weight = 2159.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133923 restraints weight = 1565.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1636  Z= 0.116
  Angle     :  0.498   6.490   2265  Z= 0.243
  Chirality :  0.042   0.122    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.785  10.816    263
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.22 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  4.08 (0.56), residues: 248
  helix:  3.56 (0.37), residues: 196
  sheet:  None (None), residues: 0
  loop : -1.03 (0.89), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.004   0.001   PHE A 161 
 TYR   0.009   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  142)
  hydrogen bonds       : angle       3.49162 (  426)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.21496 (    2)
  covalent geometry    : bond        0.00252 ( 1635)
  covalent geometry    : angle       0.49820 ( 2263)

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

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

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  496 Ramachandran restraints generated.
    248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8823 (tp) cc_final: 0.8506 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 24
  average time/residue: 0.0604
  time to fit residues: 2.0431
Evaluate side-chains
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0370
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.145667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.132050 restraints weight = 3680.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.133807 restraints weight = 2214.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.135093 restraints weight = 1611.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   1636  Z= 0.113
  Angle     :  0.501   6.652   2265  Z= 0.245
  Chirality :  0.041   0.123    287
  Planarity :  0.005   0.044    298
  Dihedral  :  2.810  11.334    263
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.22 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  4.05 (0.56), residues: 248
  helix:  3.56 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.04 (0.89), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 
 PHE   0.004   0.001   PHE A 161 
 TYR   0.009   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  142)
  hydrogen bonds       : angle       3.51282 (  426)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       0.27488 (    2)
  covalent geometry    : bond        0.00240 ( 1635)
  covalent geometry    : angle       0.50087 ( 2263)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 940.69 seconds
wall clock time: 17 minutes 10.86 seconds (1030.86 seconds total)