Starting phenix.real_space_refine
on Tue Mar  3 12:23:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1b_33559/03_2026/7y1b_33559_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1b_33559/03_2026/7y1b_33559.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2026/7y1b_33559.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2026/7y1b_33559.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2026/7y1b_33559_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2026/7y1b_33559_neut.cif"
  }
  resolution = 3.23
  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=  -0.000 sd=   0.027
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      16      5.16       5
     C    2587      2.51       5
     N     698      2.21       5
     O     836      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4137
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 868
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1608
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1661
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
  Time building chain proxies: 0.94, per 1000 atoms: 0.23
  Number of scatterers: 4137
  At special positions: 0
  Unit cell: (76.44, 65.52, 107.52, 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      16     16.00
     O     836      8.00
     N     698      7.00
     C    2587      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 163 " - pdb=" SG  CYS H 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 154 " - pdb=" SG  CYS L 214 " distance=2.04

  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: 0.30
  Conformation dependent library (CDL) restraints added in 131.6 milliseconds
  

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1006

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 12 sheets defined
      3.7% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 4.294A  pdb=" N   TYR H  51 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 81 through 84
      removed outlier: 4.213A  pdb=" N   LYS H  84 " --> pdb=" O   GLU H  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 81 through 84'
    Processing helix  chain 'L' and resid 99 through 103
      removed outlier: 4.095A  pdb=" N   VAL L 103 " --> pdb=" O   PRO L 100 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 143 through 148
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151
      removed outlier: 3.964A  pdb=" N   THR A 186 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 24
    Processing sheet with id=AA4, first strand: chain 'H' and resid 28 through 31
      removed outlier: 6.558A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'H' and resid 78 through 79
      removed outlier: 6.687A  pdb=" N   TRP H  55 " --> pdb=" O   ILE H  67 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   MET H  69 " --> pdb=" O   ILE H  53 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE H  53 " --> pdb=" O   MET H  69 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR H 125 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 143 through 147
    Processing sheet with id=AA7, first strand: chain 'H' and resid 143 through 147
    Processing sheet with id=AA8, first strand: chain 'H' and resid 174 through 177
    Processing sheet with id=AA9, first strand: chain 'L' and resid 25 through 27
    Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 33
      removed outlier: 3.832A  pdb=" N   TYR L 106 " --> pdb=" O   THR L 122 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   GLN L  57 " --> pdb=" O   LEU L  66 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   LEU L  66 " --> pdb=" O   GLN L  57 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 134 through 138
      removed outlier: 3.922A  pdb=" N   ASN L 157 " --> pdb=" O   THR L 134 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 173 through 174
      removed outlier: 6.278A  pdb=" N   HIS L 218 " --> pdb=" O   SER L 223 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   SER L 223 " --> pdb=" O   HIS L 218 " (cutoff:3.500A)

    164 hydrogen bonds defined for protein.
    408 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: 0.57

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1331
        1.34 -     1.46: 1049
        1.46 -     1.58: 1832
        1.58 -     1.70: 0
        1.70 -     1.82: 21
  Bond restraints: 4233
  Sorted by residual:
  bond pdb=" CG  PRO H  72 "
       pdb=" CD  PRO H  72 "
    ideal  model  delta    sigma   weight residual
    1.503  1.464  0.039 3.40e-02 8.65e+02 1.29e+00
  bond pdb=" CG  PRO A 133 "
       pdb=" CD  PRO A 133 "
    ideal  model  delta    sigma   weight residual
    1.512  1.482  0.030 2.70e-02 1.37e+03 1.22e+00
  bond pdb=" CZ  ARG H 117 "
       pdb=" NH2 ARG H 117 "
    ideal  model  delta    sigma   weight residual
    1.330  1.317  0.013 1.30e-02 5.92e+03 1.07e+00
  bond pdb=" CB  PRO L 161 "
       pdb=" CG  PRO L 161 "
    ideal  model  delta    sigma   weight residual
    1.492  1.443  0.049 5.00e-02 4.00e+02 9.56e-01
  bond pdb=" CB  GLN H  25 "
       pdb=" CG  GLN H  25 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.95e-01
  ... (remaining 4228 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 5475
        1.25 -     2.50: 227
        2.50 -     3.75: 45
        3.75 -     5.00: 13
        5.00 -     6.24: 3
  Bond angle restraints: 5763
  Sorted by residual:
  angle pdb=" C   TYR L  70 "
        pdb=" N   VAL L  71 "
        pdb=" CA  VAL L  71 "
      ideal   model   delta    sigma   weight residual
     120.46  116.81    3.65 1.37e+00 5.33e-01 7.11e+00
  angle pdb=" N   TYR L 160 "
        pdb=" CA  TYR L 160 "
        pdb=" C   TYR L 160 "
      ideal   model   delta    sigma   weight residual
     109.81  115.61   -5.80 2.21e+00 2.05e-01 6.88e+00
  angle pdb=" N   TYR L  70 "
        pdb=" CA  TYR L  70 "
        pdb=" C   TYR L  70 "
      ideal   model   delta    sigma   weight residual
     108.23  104.68    3.55 1.38e+00 5.25e-01 6.63e+00
  angle pdb=" CA  TYR A 132 "
        pdb=" CB  TYR A 132 "
        pdb=" CG  TYR A 132 "
      ideal   model   delta    sigma   weight residual
     113.90  109.57    4.33 1.80e+00 3.09e-01 5.80e+00
  angle pdb=" N   SER L  72 "
        pdb=" CA  SER L  72 "
        pdb=" C   SER L  72 "
      ideal   model   delta    sigma   weight residual
     110.80  115.76   -4.96 2.13e+00 2.20e-01 5.43e+00
  ... (remaining 5758 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 2277
       17.56 -    35.12: 214
       35.12 -    52.68: 39
       52.68 -    70.24: 7
       70.24 -    87.79: 3
  Dihedral angle restraints: 2540
    sinusoidal: 973
      harmonic: 1567
  Sorted by residual:
  dihedral pdb=" CA  PRO H 170 "
           pdb=" C   PRO H 170 "
           pdb=" N   GLU H 171 "
           pdb=" CA  GLU H 171 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.12  -17.88     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  TYR H  79 "
           pdb=" C   TYR H  79 "
           pdb=" N   ASN H  80 "
           pdb=" CA  ASN H  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.26   17.74     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  LEU H 102 "
           pdb=" C   LEU H 102 "
           pdb=" N   SER H 103 "
           pdb=" CA  SER H 103 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.57  -17.43     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 2537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 351
       0.032 -    0.064: 210
       0.064 -    0.095: 46
       0.095 -    0.127: 37
       0.127 -    0.159: 9
  Chirality restraints: 653
  Sorted by residual:
  chirality pdb=" CA  ILE L  68 "
            pdb=" N   ILE L  68 "
            pdb=" C   ILE L  68 "
            pdb=" CB  ILE L  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CA  ILE A 175 "
            pdb=" N   ILE A 175 "
            pdb=" C   ILE A 175 "
            pdb=" CB  ILE A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.87e-01
  chirality pdb=" CA  ILE H  70 "
            pdb=" N   ILE H  70 "
            pdb=" C   ILE H  70 "
            pdb=" CB  ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  ... (remaining 650 not shown)

  Planarity restraints: 735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 167 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.77e+00
        pdb=" N   PRO A 168 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 168 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 168 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 132 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO A 133 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 133 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 133 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS H  71 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO H  72 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO H  72 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO H  72 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 732 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1514
        2.85 -     3.36: 3279
        3.36 -     3.88: 6231
        3.88 -     4.39: 7142
        4.39 -     4.90: 13496
  Nonbonded interactions: 31662
  Sorted by model distance:
  nonbonded pdb=" O   GLY H 156 "
            pdb=" OG  SER H 157 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" N   ASP A 179 "
            pdb=" OD2 ASP A 183 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NZ  LYS H  86 "
            pdb=" O   SER H 104 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   SER L 188 "
            pdb=" OG  SER L 188 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   SER L  97 "
            pdb=" OG  SER L  97 "
     model   vdw
     2.371 3.040
  ... (remaining 31657 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.540
  Find NCS groups from input model:        0.010
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
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      :  0.006   0.049   4238  Z= 0.240
  Angle     :  0.637   6.244   5773  Z= 0.341
  Chirality :  0.047   0.159    653
  Planarity :  0.005   0.060    735
  Dihedral  : 14.264  87.794   1519
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -1.42 (0.35), residues: 533
  helix: -3.89 (1.04), residues: 12
  sheet: -0.13 (0.31), residues: 258
  loop : -1.65 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 106 
 TYR   0.022   0.002   TYR A 132 
 PHE   0.009   0.002   PHE L 155 
 TRP   0.015   0.002   TRP H  66 
 HIS   0.005   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 4233)
  covalent geometry    : angle       0.63564 ( 5763)
  SS BOND              : bond        0.00471 (    5)
  SS BOND              : angle       1.07550 (   10)
  hydrogen bonds       : bond        0.11059 (  150)
  hydrogen bonds       : angle       5.95813 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0748
  time to fit residues: 4.9280
Evaluate side-chains
  48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
** L  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.127330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109810 restraints weight = 5631.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.16
r_work: 0.3256 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4238  Z= 0.134
  Angle     :  0.615   7.723   5773  Z= 0.313
  Chirality :  0.045   0.161    653
  Planarity :  0.005   0.064    735
  Dihedral  :  4.643  19.094    578
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  5.27 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.92 (0.36), residues: 533
  helix: -3.65 (0.97), residues: 13
  sheet:  0.20 (0.31), residues: 261
  loop : -1.28 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 106 
 TYR   0.014   0.001   TYR A 132 
 PHE   0.009   0.001   PHE H 189 
 TRP   0.011   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4233)
  covalent geometry    : angle       0.61469 ( 5763)
  SS BOND              : bond        0.00355 (    5)
  SS BOND              : angle       0.77452 (   10)
  hydrogen bonds       : bond        0.02805 (  150)
  hydrogen bonds       : angle       5.32637 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8454 (mm-40)
  outliers start: 3
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0680
  time to fit residues: 4.6400
Evaluate side-chains
  49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain L residue  200 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
** L  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.110202 restraints weight = 5526.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.09
r_work: 0.3239 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4238  Z= 0.186
  Angle     :  0.640   7.928   5773  Z= 0.326
  Chirality :  0.046   0.161    653
  Planarity :  0.005   0.063    735
  Dihedral  :  4.745  18.896    578
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  9.70 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.94 (0.36), residues: 533
  helix: -3.66 (0.86), residues: 13
  sheet:  0.10 (0.31), residues: 259
  loop : -1.18 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 106 
 TYR   0.015   0.001   TYR A 132 
 PHE   0.008   0.002   PHE A 139 
 TRP   0.013   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 4233)
  covalent geometry    : angle       0.63985 ( 5763)
  SS BOND              : bond        0.00367 (    5)
  SS BOND              : angle       0.89433 (   10)
  hydrogen bonds       : bond        0.03032 (  150)
  hydrogen bonds       : angle       5.37399 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 50
  average time/residue: 0.0751
  time to fit residues: 4.7295
Evaluate side-chains
  49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain L residue  200 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 50 optimal weight:    0.0000
   chunk 15 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
** L  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.112517 restraints weight = 5521.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.15
r_work: 0.3294 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4238  Z= 0.105
  Angle     :  0.556   6.449   5773  Z= 0.282
  Chirality :  0.044   0.159    653
  Planarity :  0.005   0.061    735
  Dihedral  :  4.252  18.345    578
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.55 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.64 (0.37), residues: 533
  helix: -3.49 (0.92), residues: 14
  sheet:  0.36 (0.32), residues: 258
  loop : -1.04 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 106 
 TYR   0.012   0.001   TYR A 132 
 PHE   0.009   0.001   PHE A 139 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4233)
  covalent geometry    : angle       0.55542 ( 5763)
  SS BOND              : bond        0.00310 (    5)
  SS BOND              : angle       0.66665 (   10)
  hydrogen bonds       : bond        0.02410 (  150)
  hydrogen bonds       : angle       4.93676 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 51
  average time/residue: 0.0739
  time to fit residues: 4.7532
Evaluate side-chains
  48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0370
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
A 115 HIS
L  54 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.135546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.118236 restraints weight = 5373.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.09
r_work: 0.3288 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4238  Z= 0.111
  Angle     :  0.552   6.287   5773  Z= 0.280
  Chirality :  0.044   0.151    653
  Planarity :  0.005   0.062    735
  Dihedral  :  4.168  18.061    578
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.39 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.45 (0.37), residues: 533
  helix: -3.44 (0.91), residues: 14
  sheet:  0.49 (0.32), residues: 259
  loop : -0.90 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 106 
 TYR   0.010   0.001   TYR L  70 
 PHE   0.007   0.001   PHE A 139 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4233)
  covalent geometry    : angle       0.55186 ( 5763)
  SS BOND              : bond        0.00302 (    5)
  SS BOND              : angle       0.63450 (   10)
  hydrogen bonds       : bond        0.02413 (  150)
  hydrogen bonds       : angle       4.87411 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7787 (tt0)
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 0.0739
  time to fit residues: 4.7426
Evaluate side-chains
  47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
H  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.128359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.110555 restraints weight = 5645.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.17
r_work: 0.3253 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4238  Z= 0.169
  Angle     :  0.598   6.604   5773  Z= 0.305
  Chirality :  0.045   0.154    653
  Planarity :  0.005   0.062    735
  Dihedral  :  4.447  18.545    578
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 12.87 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.47 (0.37), residues: 533
  helix: -3.58 (0.80), residues: 14
  sheet:  0.44 (0.32), residues: 259
  loop : -0.86 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 106 
 TYR   0.014   0.001   TYR L  70 
 PHE   0.008   0.002   PHE L 229 
 TRP   0.013   0.001   TRP A 138 
 HIS   0.004   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4233)
  covalent geometry    : angle       0.59803 ( 5763)
  SS BOND              : bond        0.00354 (    5)
  SS BOND              : angle       0.77654 (   10)
  hydrogen bonds       : bond        0.02785 (  150)
  hydrogen bonds       : angle       5.11197 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8139 (tt0) cc_final: 0.7768 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 48
  average time/residue: 0.0697
  time to fit residues: 4.3889
Evaluate side-chains
  46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.138649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121872 restraints weight = 5402.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.04
r_work: 0.3337 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4238  Z= 0.090
  Angle     :  0.520   5.808   5773  Z= 0.265
  Chirality :  0.043   0.152    653
  Planarity :  0.005   0.062    735
  Dihedral  :  3.934  17.437    578
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.29 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.14 (0.38), residues: 533
  helix: -3.46 (0.91), residues: 14
  sheet:  0.73 (0.33), residues: 259
  loop : -0.72 (0.41), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 106 
 TYR   0.007   0.001   TYR L  70 
 PHE   0.009   0.001   PHE A 139 
 TRP   0.007   0.001   TRP H  66 
 HIS   0.003   0.001   HIS L  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 4233)
  covalent geometry    : angle       0.52026 ( 5763)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       0.59211 (   10)
  hydrogen bonds       : bond        0.02178 (  150)
  hydrogen bonds       : angle       4.67926 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.100 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 48
  average time/residue: 0.0716
  time to fit residues: 4.5077
Evaluate side-chains
  48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Chi-restraints excluded: chain L residue  217 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   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 = 0.3589 r_free = 0.3589 target = 0.134874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.118259 restraints weight = 5363.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.02
r_work: 0.3226 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4238  Z= 0.134
  Angle     :  0.573   6.114   5773  Z= 0.291
  Chirality :  0.044   0.170    653
  Planarity :  0.005   0.061    735
  Dihedral  :  4.195  17.385    578
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 13.92 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.10 (0.38), residues: 533
  helix: -3.44 (0.89), residues: 14
  sheet:  0.75 (0.33), residues: 258
  loop : -0.70 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 106 
 TYR   0.011   0.001   TYR L  70 
 PHE   0.007   0.001   PHE L 229 
 TRP   0.012   0.001   TRP A 138 
 HIS   0.004   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4233)
  covalent geometry    : angle       0.57277 ( 5763)
  SS BOND              : bond        0.00318 (    5)
  SS BOND              : angle       0.68543 (   10)
  hydrogen bonds       : bond        0.02534 (  150)
  hydrogen bonds       : angle       4.85843 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.165 
Fit side-chains
REVERT: H  194 GLN cc_start: 0.7562 (pt0) cc_final: 0.7266 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0592
  time to fit residues: 3.6814
Evaluate side-chains
  46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Chi-restraints excluded: chain L residue  217 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.135556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.118820 restraints weight = 5404.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.03
r_work: 0.3270 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4238  Z= 0.120
  Angle     :  0.559   6.030   5773  Z= 0.284
  Chirality :  0.044   0.165    653
  Planarity :  0.005   0.061    735
  Dihedral  :  4.122  17.124    578
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.35 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole: -0.02 (0.38), residues: 533
  helix: -3.44 (0.88), residues: 14
  sheet:  0.85 (0.33), residues: 261
  loop : -0.71 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 106 
 TYR   0.011   0.001   TYR L  70 
 PHE   0.008   0.001   PHE A 139 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4233)
  covalent geometry    : angle       0.55885 ( 5763)
  SS BOND              : bond        0.00311 (    5)
  SS BOND              : angle       0.66259 (   10)
  hydrogen bonds       : bond        0.02429 (  150)
  hydrogen bonds       : angle       4.82108 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  129 ASP cc_start: 0.6788 (p0) cc_final: 0.6529 (p0)
REVERT: H  194 GLN cc_start: 0.7502 (pt0) cc_final: 0.7295 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 50
  average time/residue: 0.0642
  time to fit residues: 4.2581
Evaluate side-chains
  48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Chi-restraints excluded: chain L residue  217 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 22 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0670
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3616 r_free = 0.3616 target = 0.137324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120637 restraints weight = 5303.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.02
r_work: 0.3317 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4238  Z= 0.103
  Angle     :  0.541   5.870   5773  Z= 0.276
  Chirality :  0.043   0.163    653
  Planarity :  0.005   0.061    735
  Dihedral  :  3.997  16.676    578
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 15.19 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  0.09 (0.38), residues: 533
  helix: -3.35 (0.92), residues: 14
  sheet:  0.97 (0.33), residues: 260
  loop : -0.69 (0.41), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 106 
 TYR   0.008   0.001   TYR L  70 
 PHE   0.008   0.001   PHE A 139 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4233)
  covalent geometry    : angle       0.54059 ( 5763)
  SS BOND              : bond        0.00308 (    5)
  SS BOND              : angle       0.60448 (   10)
  hydrogen bonds       : bond        0.02299 (  150)
  hydrogen bonds       : angle       4.70931 (  408)

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

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

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1066 Ramachandran restraints generated.
    533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.154 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 46
  average time/residue: 0.0750
  time to fit residues: 4.4674
Evaluate side-chains
  46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.134849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118139 restraints weight = 5391.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.03
r_work: 0.3208 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4238  Z= 0.132
  Angle     :  0.572   6.120   5773  Z= 0.290
  Chirality :  0.044   0.163    653
  Planarity :  0.005   0.059    735
  Dihedral  :  4.150  16.928    578
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.98 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  0.03 (0.38), residues: 533
  helix: -3.45 (0.84), residues: 14
  sheet:  0.88 (0.33), residues: 261
  loop : -0.67 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 106 
 TYR   0.012   0.001   TYR L  70 
 PHE   0.007   0.001   PHE L 229 
 TRP   0.011   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4233)
  covalent geometry    : angle       0.57164 ( 5763)
  SS BOND              : bond        0.00325 (    5)
  SS BOND              : angle       0.65922 (   10)
  hydrogen bonds       : bond        0.02526 (  150)
  hydrogen bonds       : angle       4.88615 (  408)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1219.13 seconds
wall clock time: 21 minutes 31.43 seconds (1291.43 seconds total)