Starting phenix.real_space_refine
on Wed Jun  4 09:56:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w77_37336/06_2025/8w77_37336_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w77_37336/06_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_37336/06_2025/8w77_37336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w77_37336/06_2025/8w77_37336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w77_37336/06_2025/8w77_37336_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w77_37336/06_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 2.28, per 1000 atoms: 1.42
  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: 0.47
  Conformation dependent library (CDL) restraints added in 251.8 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: 0.19
  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: 0.44

  Time building geometry restraints manager: 0.55 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:             1.870
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.450
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.110
-------------------------------------------------------------------------------
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  : 0.166 
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: 0.0517
  time to fit residues: 2.0416
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  : 0.168 
-------------------------------------------------------------------------------
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:    0.0030
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.5528

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.148890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.135873 restraints weight = 3544.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.137365 restraints weight = 2228.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138375 restraints weight = 1668.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1022

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= 0.124
  Angle     :  0.499   4.969   2265  Z= 0.259
  Chirality :  0.041   0.124    287
  Planarity :  0.006   0.050    298
  Dihedral  :  3.095  11.201    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:  3.35 (0.56), residues: 248
  helix:  3.00 (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   0.003   0.001   HIS A 183 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.011   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04316 (  142)
  hydrogen bonds       : angle       4.29609 (  426)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       0.15021 (    2)
  covalent geometry    : bond        0.00253 ( 1635)
  covalent geometry    : angle       0.49906 ( 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  : 0.201 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8909 (tp) cc_final: 0.8583 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0462
  time to fit residues: 1.7914
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  : 0.202 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   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:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.142613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.129317 restraints weight = 3535.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.130770 restraints weight = 2228.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.131790 restraints weight = 1661.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1636  Z= 0.161
  Angle     :  0.543   5.125   2265  Z= 0.285
  Chirality :  0.043   0.124    287
  Planarity :  0.006   0.049    298
  Dihedral  :  3.297  13.035    263
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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:  3.34 (0.55), residues: 248
  helix:  3.06 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.22 (0.85), residues: 54

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   0.007   0.001   PHE A 161 
 TYR   0.019   0.002   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05325 (  142)
  hydrogen bonds       : angle       4.22157 (  426)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.27592 (    2)
  covalent geometry    : bond        0.00354 ( 1635)
  covalent geometry    : angle       0.54328 ( 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
  23 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8934 (tp) cc_final: 0.8613 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0405
  time to fit residues: 1.4382
Evaluate side-chains
  22 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0570
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.4004 r_free = 0.4004 target = 0.145590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.132140 restraints weight = 3513.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.133691 restraints weight = 2167.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.134763 restraints weight = 1610.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1663

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= 0.119
  Angle     :  0.489   5.026   2265  Z= 0.249
  Chirality :  0.042   0.124    287
  Planarity :  0.005   0.047    298
  Dihedral  :  3.027  11.702    263
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  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:  3.67 (0.56), residues: 248
  helix:  3.28 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.05 (0.87), residues: 54

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  64 
 TYR   0.008   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  142)
  hydrogen bonds       : angle       3.87543 (  426)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       0.30248 (    2)
  covalent geometry    : bond        0.00247 ( 1635)
  covalent geometry    : angle       0.48890 ( 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  : 0.180 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8879 (tp) cc_final: 0.8568 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 23
  average time/residue: 0.0429
  time to fit residues: 1.5620
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  : 0.177 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 22 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4005 r_free = 0.4005 target = 0.145566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.132138 restraints weight = 3548.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133694 restraints weight = 2166.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.134895 restraints weight = 1607.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1831

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= 0.119
  Angle     :  0.491   5.055   2265  Z= 0.248
  Chirality :  0.042   0.123    287
  Planarity :  0.005   0.046    298
  Dihedral  :  2.951  11.411    263
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 1.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 15.56 %
    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:  3.72 (0.56), residues: 248
  helix:  3.33 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.18 (0.88), 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   0.004   0.001   PHE A 161 
 TYR   0.010   0.001   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  142)
  hydrogen bonds       : angle       3.74974 (  426)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       0.29781 (    2)
  covalent geometry    : bond        0.00258 ( 1635)
  covalent geometry    : angle       0.49135 ( 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
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8845 (tp) cc_final: 0.8547 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0443
  time to fit residues: 1.7881
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  : 0.171 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0670
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8920

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.142897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.129330 restraints weight = 3587.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.131052 restraints weight = 2151.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132035 restraints weight = 1587.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   1636  Z= 0.143
  Angle     :  0.520   5.151   2265  Z= 0.265
  Chirality :  0.043   0.125    287
  Planarity :  0.005   0.045    298
  Dihedral  :  3.100  12.515    263
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 15.56 %
    Favored  : 78.89 %
  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:  3.51 (0.56), residues: 248
  helix:  3.23 (0.38), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.36 (0.85), 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   0.013   0.001   TYR A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04775 (  142)
  hydrogen bonds       : angle       3.88949 (  426)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.28578 (    2)
  covalent geometry    : bond        0.00317 ( 1635)
  covalent geometry    : angle       0.52037 ( 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
  28 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8848 (tp) cc_final: 0.8545 (tt)
  outliers start: 5
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0441
  time to fit residues: 1.7804
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
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:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0470
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0030
   overall best weight:    0.4488

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.146236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.132769 restraints weight = 3522.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.134373 restraints weight = 2143.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.135589 restraints weight = 1585.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2008

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= 0.109
  Angle     :  0.490   5.644   2265  Z= 0.243
  Chirality :  0.041   0.123    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.884  11.107    263
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 16.67 %
    Favored  : 78.89 %
  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:  3.87 (0.56), residues: 248
  helix:  3.45 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.20 (0.87), 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   0.004   0.000   PHE A  64 
 TYR   0.007   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03869 (  142)
  hydrogen bonds       : angle       3.60845 (  426)
  SS BOND              : bond        0.00243 (    1)
  SS BOND              : angle       0.47811 (    2)
  covalent geometry    : bond        0.00226 ( 1635)
  covalent geometry    : angle       0.48977 ( 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
  29 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8835 (tp) cc_final: 0.8527 (tt)
  outliers start: 4
  outliers final: 4
  residues processed: 28
  average time/residue: 0.0443
  time to fit residues: 1.9080
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  164 LEU
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:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.142347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.129027 restraints weight = 3487.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.130621 restraints weight = 2192.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.131637 restraints weight = 1610.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2050

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= 0.127
  Angle     :  0.511   5.856   2265  Z= 0.255
  Chirality :  0.042   0.123    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.971  11.791    263
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 16.67 %
    Favored  : 78.89 %
  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:  3.77 (0.56), residues: 248
  helix:  3.40 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.32 (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 107 
 PHE   0.005   0.001   PHE A 161 
 TYR   0.010   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04345 (  142)
  hydrogen bonds       : angle       3.70385 (  426)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.26287 (    2)
  covalent geometry    : bond        0.00282 ( 1635)
  covalent geometry    : angle       0.51132 ( 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
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8827 (tp) cc_final: 0.8534 (tt)
  outliers start: 4
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0418
  time to fit residues: 1.6783
Evaluate side-chains
  27 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  164 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 22 optimal weight:    0.0670
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0870
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.4096

-------------------------------------------------------------------------------
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 = 0.145911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.132496 restraints weight = 3610.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.134151 restraints weight = 2231.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.135362 restraints weight = 1632.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2115

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= 0.107
  Angle     :  0.493   6.382   2265  Z= 0.242
  Chirality :  0.041   0.123    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.837  11.421    263
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 18.89 %
    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:  3.92 (0.56), residues: 248
  helix:  3.48 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.12 (0.89), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  28 
 HIS   0.001   0.001   HIS A 275 
 PHE   0.004   0.000   PHE A  64 
 TYR   0.007   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  142)
  hydrogen bonds       : angle       3.52488 (  426)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       0.45411 (    2)
  covalent geometry    : bond        0.00221 ( 1635)
  covalent geometry    : angle       0.49290 ( 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: 4
    poor density    : 23
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8803 (tp) cc_final: 0.8519 (tt)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0538
  time to fit residues: 2.1728
Evaluate side-chains
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  164 LEU
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:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.141202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.127725 restraints weight = 3565.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.129396 restraints weight = 2201.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.130441 restraints weight = 1614.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2164

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= 0.140
  Angle     :  0.528   6.300   2265  Z= 0.264
  Chirality :  0.043   0.123    287
  Planarity :  0.005   0.044    298
  Dihedral  :  3.032  12.157    263
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.00 %
    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:  3.73 (0.56), residues: 248
  helix:  3.38 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.37 (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 107 
 PHE   0.006   0.001   PHE A 161 
 TYR   0.013   0.001   TYR A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 (  142)
  hydrogen bonds       : angle       3.76503 (  426)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.31648 (    2)
  covalent geometry    : bond        0.00317 ( 1635)
  covalent geometry    : angle       0.52855 ( 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
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8847 (tp) cc_final: 0.8551 (tt)
  outliers start: 3
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0460
  time to fit residues: 1.7852
Evaluate side-chains
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  164 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.144047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.130394 restraints weight = 3677.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.132198 restraints weight = 2170.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.133307 restraints weight = 1580.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2192

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= 0.116
  Angle     :  0.506   6.682   2265  Z= 0.250
  Chirality :  0.042   0.125    287
  Planarity :  0.005   0.044    298
  Dihedral  :  2.920  11.491    263
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 18.89 %
    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:  3.88 (0.56), residues: 248
  helix:  3.45 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.15 (0.88), 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        0.04151 (  142)
  hydrogen bonds       : angle       3.63486 (  426)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.32855 (    2)
  covalent geometry    : bond        0.00247 ( 1635)
  covalent geometry    : angle       0.50564 ( 2263)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 976.74 seconds
wall clock time: 17 minutes 48.69 seconds (1068.69 seconds total)