Starting phenix.real_space_refine
on Fri Aug 22 12:37:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w77_37336/08_2025/8w77_37336_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w77_37336/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w77_37336/08_2025/8w77_37336_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w77_37336/08_2025/8w77_37336_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w77_37336/08_2025/8w77_37336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w77_37336/08_2025/8w77_37336.map"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 5, 'HIS:plan': 5, 'TRP:plan': 2, 'PHE:plan': 8, 'TYR:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 191
  Time building chain proxies: 0.56, per 1000 atoms: 0.35
  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: 0.09
  Conformation dependent library (CDL) restraints added in 55.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.06
  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: 0.17

  Time building geometry restraints manager: 0.13 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:             1.840
  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:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     3.000
  Find NCS groups from input model:        0.000
  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:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.980
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 TYR   0.008   0.001   TYR A 134 
 PHE   0.004   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 183 

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

*********************** 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  : 0.082 
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: 0.0155
  time to fit residues: 0.6292
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  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.147248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.133978 restraints weight = 3597.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.135530 restraints weight = 2305.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.136368 restraints weight = 1723.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.137148 restraints weight = 1453.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.137469 restraints weight = 1281.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1044

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= 0.132
  Angle     :  0.509   5.043   2265  Z= 0.266
  Chirality :  0.042   0.123    287
  Planarity :  0.006   0.051    298
  Dihedral  :  3.147  11.652    263
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.29 (0.56), residues: 248
  helix:  2.96 (0.38), residues: 194
  sheet:  None (None), residues: 0
  loop : -0.96 (0.88), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.001   TYR A 130 
 PHE   0.012   0.001   PHE A  64 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 1635)
  covalent geometry    : angle       0.50953 ( 2263)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.14807 (    2)
  hydrogen bonds       : bond        0.04499 (  142)
  hydrogen bonds       : angle       4.32190 (  426)

*********************** 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
  25 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.034 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8931 (tp) cc_final: 0.8596 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0103
  time to fit residues: 0.3882
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  : 0.034 
-------------------------------------------------------------------------------
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 19 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.141533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.128108 restraints weight = 3595.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.129630 restraints weight = 2262.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.130679 restraints weight = 1679.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.131359 restraints weight = 1377.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.131513 restraints weight = 1215.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1668

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= 0.164
  Angle     :  0.546   5.133   2265  Z= 0.287
  Chirality :  0.043   0.124    287
  Planarity :  0.006   0.050    298
  Dihedral  :  3.333  13.062    263
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 2.87
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.25 (0.55), residues: 248
  helix:  2.99 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.20 (0.85), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.019   0.002   TYR A 130 
 PHE   0.007   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.002   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 1635)
  covalent geometry    : angle       0.54577 ( 2263)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       0.28019 (    2)
  hydrogen bonds       : bond        0.05430 (  142)
  hydrogen bonds       : angle       4.28077 (  426)

*********************** 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  : 0.064 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8913 (tp) cc_final: 0.8590 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0211
  time to fit residues: 0.7099
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  : 0.036 
-------------------------------------------------------------------------------
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 13 optimal weight:    5.9990
   chunk 24 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.137877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.124214 restraints weight = 3656.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.125841 restraints weight = 2291.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.126928 restraints weight = 1719.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.127309 restraints weight = 1417.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.127871 restraints weight = 1293.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   1636  Z= 0.197
  Angle     :  0.578   5.324   2265  Z= 0.305
  Chirality :  0.045   0.129    287
  Planarity :  0.006   0.048    298
  Dihedral  :  3.625  14.776    263
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.55), residues: 248
  helix:  2.73 (0.37), residues: 192
  sheet:  None (None), residues: 0
  loop : -1.21 (0.84), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.021   0.002   TYR A 130 
 PHE   0.008   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.006   0.002   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 1635)
  covalent geometry    : angle       0.57860 ( 2263)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.43474 (    2)
  hydrogen bonds       : bond        0.06016 (  142)
  hydrogen bonds       : angle       4.42958 (  426)

*********************** 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: 4
    poor density    : 20
  time to evaluate  : 0.066 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 23
  average time/residue: 0.0191
  time to fit residues: 0.6862
Evaluate side-chains
  22 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.141606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.127920 restraints weight = 3598.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129579 restraints weight = 2178.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.130745 restraints weight = 1590.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.131220 restraints weight = 1291.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.131227 restraints weight = 1166.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2103

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= 0.143
  Angle     :  0.520   5.124   2265  Z= 0.269
  Chirality :  0.043   0.126    287
  Planarity :  0.005   0.047    298
  Dihedral  :  3.304  12.180    263
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.89 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.23 (0.56), residues: 248
  helix:  3.00 (0.37), residues: 193
  sheet:  None (None), residues: 0
  loop : -1.24 (0.86), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.001   TYR A 130 
 PHE   0.006   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 1635)
  covalent geometry    : angle       0.52060 ( 2263)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.32755 (    2)
  hydrogen bonds       : bond        0.05029 (  142)
  hydrogen bonds       : angle       4.07645 (  426)

*********************** 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
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8922 (tp) cc_final: 0.8608 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0183
  time to fit residues: 0.7253
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  : 0.063 
-------------------------------------------------------------------------------
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 15 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.142880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.129274 restraints weight = 3605.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.130953 restraints weight = 2197.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.132028 restraints weight = 1602.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.132886 restraints weight = 1301.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.133275 restraints weight = 1133.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2122

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= 0.131
  Angle     :  0.509   5.143   2265  Z= 0.258
  Chirality :  0.042   0.125    287
  Planarity :  0.005   0.046    298
  Dihedral  :  3.154  12.405    263
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.78 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.38 (0.56), residues: 248
  helix:  3.12 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.34 (0.86), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR A 134 
 PHE   0.005   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 1635)
  covalent geometry    : angle       0.50876 ( 2263)
  SS BOND              : bond        0.00191 (    1)
  SS BOND              : angle       0.37630 (    2)
  hydrogen bonds       : bond        0.04635 (  142)
  hydrogen bonds       : angle       3.88491 (  426)

*********************** 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: 4
    poor density    : 23
  time to evaluate  : 0.062 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8881 (tp) cc_final: 0.8574 (tt)
  outliers start: 4
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0177
  time to fit residues: 0.6977
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  : 0.064 
-------------------------------------------------------------------------------
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 6 optimal weight:    0.0040
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.4392

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.145547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132200 restraints weight = 3458.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.133901 restraints weight = 2093.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.134990 restraints weight = 1541.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.135821 restraints weight = 1253.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.136211 restraints weight = 1096.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2155

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     :  0.493   6.136   2265  Z= 0.244
  Chirality :  0.041   0.124    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.906  11.030    263
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.00 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.74 (0.56), residues: 248
  helix:  3.36 (0.38), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.23 (0.88), residues: 53

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 1635)
  covalent geometry    : angle       0.49327 ( 2263)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       0.53874 (    2)
  hydrogen bonds       : bond        0.03845 (  142)
  hydrogen bonds       : angle       3.63300 (  426)

*********************** 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
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.060 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8790 (tp) cc_final: 0.8492 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0174
  time to fit residues: 0.6846
Evaluate side-chains
  24 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.142802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.129284 restraints weight = 3522.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.130956 restraints weight = 2164.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132082 restraints weight = 1591.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132507 restraints weight = 1301.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132507 restraints weight = 1183.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2189

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= 0.135
  Angle     :  0.519   5.702   2265  Z= 0.261
  Chirality :  0.042   0.124    287
  Planarity :  0.005   0.045    298
  Dihedral  :  3.065  12.131    263
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 1.79
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.62 (0.56), residues: 248
  helix:  3.28 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.28 (0.88), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR A 134 
 PHE   0.005   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 1635)
  covalent geometry    : angle       0.51964 ( 2263)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.27747 (    2)
  hydrogen bonds       : bond        0.04543 (  142)
  hydrogen bonds       : angle       3.80443 (  426)

*********************** 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  : 0.059 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8870 (tp) cc_final: 0.8568 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 24
  average time/residue: 0.0165
  time to fit residues: 0.6242
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  : 0.058 
-------------------------------------------------------------------------------
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 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.142602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.129009 restraints weight = 3535.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.130584 restraints weight = 2138.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.131702 restraints weight = 1589.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.132443 restraints weight = 1302.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132699 restraints weight = 1152.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2237

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= 0.130
  Angle     :  0.515   6.093   2265  Z= 0.258
  Chirality :  0.042   0.125    287
  Planarity :  0.005   0.045    298
  Dihedral  :  3.051  11.715    263
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.67 (0.56), residues: 248
  helix:  3.28 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.17 (0.89), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR A 134 
 PHE   0.005   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 1635)
  covalent geometry    : angle       0.51471 ( 2263)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.29758 (    2)
  hydrogen bonds       : bond        0.04535 (  142)
  hydrogen bonds       : angle       3.79145 (  426)

*********************** 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
  26 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8892 (tp) cc_final: 0.8582 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0173
  time to fit residues: 0.6866
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  : 0.061 
-------------------------------------------------------------------------------
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 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.143127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129633 restraints weight = 3537.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.131296 restraints weight = 2123.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132430 restraints weight = 1552.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.133014 restraints weight = 1256.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.133643 restraints weight = 1123.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2271

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= 0.123
  Angle     :  0.512   6.540   2265  Z= 0.254
  Chirality :  0.042   0.125    287
  Planarity :  0.005   0.044    298
  Dihedral  :  2.992  11.668    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 :  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.72 (0.56), residues: 248
  helix:  3.33 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -1.16 (0.89), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.001   TYR A 134 
 PHE   0.004   0.001   PHE A 161 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 1635)
  covalent geometry    : angle       0.51168 ( 2263)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.33530 (    2)
  hydrogen bonds       : bond        0.04309 (  142)
  hydrogen bonds       : angle       3.72148 (  426)

********************** 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  : 0.063 
Fit side-chains
REVERT: A  283 LEU cc_start: 0.8870 (tp) cc_final: 0.8557 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 24
  average time/residue: 0.0172
  time to fit residues: 0.6610
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  : 0.061 
-------------------------------------------------------------------------------
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 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0000
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4242

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.145596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.132190 restraints weight = 3515.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.133948 restraints weight = 2118.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.135026 restraints weight = 1541.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.135864 restraints weight = 1255.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.136025 restraints weight = 1086.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2320

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     :  0.495   6.801   2265  Z= 0.242
  Chirality :  0.041   0.124    287
  Planarity :  0.005   0.045    298
  Dihedral  :  2.818  10.945    263
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.89 (0.56), residues: 248
  helix:  3.40 (0.37), residues: 196
  sheet:  None (None), residues: 0
  loop : -0.99 (0.91), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR A 134 
 PHE   0.004   0.001   PHE A  64 
 TRP   0.000   0.000   TRP A  28 
 HIS   0.001   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 1635)
  covalent geometry    : angle       0.49454 ( 2263)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       0.54687 (    2)
  hydrogen bonds       : bond        0.03702 (  142)
  hydrogen bonds       : angle       3.54658 (  426)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 507.75 seconds
wall clock time: 9 minutes 35.74 seconds (575.74 seconds total)