Starting phenix.real_space_refine
on Fri Aug 22 14:32:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p0a_71067/08_2025/9p0a_71067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p0a_71067/08_2025/9p0a_71067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p0a_71067/08_2025/9p0a_71067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p0a_71067/08_2025/9p0a_71067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p0a_71067/08_2025/9p0a_71067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p0a_71067/08_2025/9p0a_71067.cif"
  }
  resolution = 4.2
  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=  -0.021 sd=   0.366
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: 3
    Type Number    sf(0)   Gaussians
     C    2442      2.51       5
     N     648      2.21       5
     O     945      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 4035
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1345
          Classifications: {'peptide': 188}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
    Chain: "D"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1345
          Classifications: {'peptide': 188}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
    Chain: "E"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1345
          Classifications: {'peptide': 188}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
  Time building chain proxies: 1.33, per 1000 atoms: 0.33
  Number of scatterers: 4035
  At special positions: 0
  Unit cell: (69.12, 64.8, 158.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     945      8.00
     N     648      7.00
     C    2442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.35
  Conformation dependent library (CDL) restraints added in 205.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 12 sheets defined
      1.4% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'C' and resid 77 through 79
      No H-bonds generated for 'chain 'C' and resid 77 through 79'
    Processing helix  chain 'C' and resid 152 through 156
      removed outlier: 3.799A  pdb=" N   ASN C 156 " --> pdb=" O   GLU C 153 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 49 through 52
      removed outlier: 3.666A  pdb=" N   ASP C  52 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 75
      removed outlier: 3.529A  pdb=" N   THR D  36 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 92
      removed outlier: 6.008A  pdb=" N   PHE C 150 " --> pdb=" O   ALA C 130 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ALA C 130 " --> pdb=" O   PHE C 150 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 170
      removed outlier: 3.867A  pdb=" N   ALA C 212 " --> pdb=" O   SER D  30 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER D  30 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 50
    Processing sheet with id=AA6, first strand: chain 'D' and resid 73 through 75
    Processing sheet with id=AA7, first strand: chain 'D' and resid 89 through 93
      removed outlier: 4.142A  pdb=" N   LEU D 184 " --> pdb=" O   PHE D  93 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   PHE D 150 " --> pdb=" O   ALA D 130 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   ALA D 130 " --> pdb=" O   PHE D 150 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 113
      removed outlier: 3.913A  pdb=" N   SER D 213 " --> pdb=" O   ASN D 108 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   SER E  30 " --> pdb=" O   ALA D 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 49 through 50
    Processing sheet with id=AB1, first strand: chain 'E' and resid 65 through 66
      removed outlier: 3.948A  pdb=" N   SER E  66 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   GLU E  73 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'E' and resid 90 through 93
      removed outlier: 3.853A  pdb=" N   LEU E 184 " --> pdb=" O   PHE E  93 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   PHE E 150 " --> pdb=" O   ALA E 130 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   ALA E 130 " --> pdb=" O   PHE E 150 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 168 through 169
      removed outlier: 4.076A  pdb=" N   SER E 213 " --> pdb=" O   ASN E 108 " (cutoff:3.500A)

    89 hydrogen bonds defined for protein.
    219 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.44

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.32: 774
        1.32 -     1.42: 882
        1.42 -     1.51: 803
        1.51 -     1.61: 1623
        1.61 -     1.70: 1
  Bond restraints: 4083
  Sorted by residual:
  bond pdb=" CB  PRO E 197 "
       pdb=" CG  PRO E 197 "
    ideal  model  delta    sigma   weight residual
    1.492  1.701 -0.209 5.00e-02 4.00e+02 1.74e+01
  bond pdb=" N   PRO E 197 "
       pdb=" CA  PRO E 197 "
    ideal  model  delta    sigma   weight residual
    1.470  1.444  0.027 1.01e-02 9.80e+03 6.92e+00
  bond pdb=" N   PRO E 197 "
       pdb=" CD  PRO E 197 "
    ideal  model  delta    sigma   weight residual
    1.473  1.503 -0.030 1.40e-02 5.10e+03 4.61e+00
  bond pdb=" CA  PRO E 197 "
       pdb=" C   PRO E 197 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 9.80e-03 1.04e+04 4.55e+00
  bond pdb=" N   PHE C  28 "
       pdb=" CA  PHE C  28 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  ... (remaining 4078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 5525
        2.98 -     5.97: 51
        5.97 -     8.95: 6
        8.95 -    11.94: 0
       11.94 -    14.92: 1
  Bond angle restraints: 5583
  Sorted by residual:
  angle pdb=" CA  PRO E 197 "
        pdb=" N   PRO E 197 "
        pdb=" CD  PRO E 197 "
      ideal   model   delta    sigma   weight residual
     112.00   97.08   14.92 1.40e+00 5.10e-01 1.14e+02
  angle pdb=" CA  ASP D  34 "
        pdb=" C   ASP D  34 "
        pdb=" N   ARG D  35 "
      ideal   model   delta    sigma   weight residual
     117.96  124.27   -6.31 1.23e+00 6.61e-01 2.63e+01
  angle pdb=" C   ASP E 152 "
        pdb=" CA  ASP E 152 "
        pdb=" CB  ASP E 152 "
      ideal   model   delta    sigma   weight residual
     116.63  110.73    5.90 1.16e+00 7.43e-01 2.59e+01
  angle pdb=" N   THR D 151 "
        pdb=" CA  THR D 151 "
        pdb=" C   THR D 151 "
      ideal   model   delta    sigma   weight residual
     113.17  119.37   -6.20 1.26e+00 6.30e-01 2.42e+01
  angle pdb=" N   PRO E 197 "
        pdb=" CD  PRO E 197 "
        pdb=" CG  PRO E 197 "
      ideal   model   delta    sigma   weight residual
     103.20   95.99    7.21 1.50e+00 4.44e-01 2.31e+01
  ... (remaining 5578 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 2127
       16.36 -    32.72: 221
       32.72 -    49.09: 42
       49.09 -    65.45: 15
       65.45 -    81.81: 4
  Dihedral angle restraints: 2409
    sinusoidal: 813
      harmonic: 1596
  Sorted by residual:
  dihedral pdb=" CA  ASN E 142 "
           pdb=" C   ASN E 142 "
           pdb=" N   SER E 143 "
           pdb=" CA  SER E 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.38  -28.62     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  ASP E 177 "
           pdb=" C   ASP E 177 "
           pdb=" N   PRO E 178 "
           pdb=" CA  PRO E 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.16   26.84     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  ASN C 142 "
           pdb=" C   ASN C 142 "
           pdb=" N   SER C 143 "
           pdb=" CA  SER C 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.26  -25.74     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 2406 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 503
       0.042 -    0.083: 104
       0.083 -    0.125: 61
       0.125 -    0.167: 12
       0.167 -    0.208: 1
  Chirality restraints: 681
  Sorted by residual:
  chirality pdb=" CA  PRO E 197 "
            pdb=" N   PRO E 197 "
            pdb=" C   PRO E 197 "
            pdb=" CB  PRO E 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE E 111 "
            pdb=" N   ILE E 111 "
            pdb=" C   ILE E 111 "
            pdb=" CB  ILE E 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CA  ILE C 111 "
            pdb=" N   ILE C 111 "
            pdb=" C   ILE C 111 "
            pdb=" CB  ILE C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.43e-01
  ... (remaining 678 not shown)

  Planarity restraints: 756
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 196 "   -0.081 5.00e-02 4.00e+02   1.11e-01 1.98e+01
        pdb=" N   PRO E 197 "    0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO E 197 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO E 197 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  35 "   -0.182 9.50e-02 1.11e+02   8.18e-02 4.23e+00
        pdb=" NE  ARG E  35 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  35 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  35 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 150 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.08e+00
        pdb=" C   PHE D 150 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   PHE D 150 "    0.013 2.00e-02 2.50e+03
        pdb=" N   THR D 151 "    0.012 2.00e-02 2.50e+03
  ... (remaining 753 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 101
        2.63 -     3.20: 4109
        3.20 -     3.76: 5501
        3.76 -     4.33: 7624
        4.33 -     4.90: 12541
  Nonbonded interactions: 29876
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 103 "
            pdb=" OG1 THR C 173 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" OG1 THR E 151 "
            pdb=" OG  SER E 183 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER D  82 "
            pdb=" O   SER E  47 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" N   SER D  83 "
            pdb=" O   SER E  46 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   GLY D 103 "
            pdb=" N   THR D 173 "
     model   vdw
     2.343 3.120
  ... (remaining 29871 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.940
  Find NCS groups from input model:        0.070
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
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   0.209   4083  Z= 0.190
  Angle     :  0.797  14.921   5583  Z= 0.506
  Chirality :  0.048   0.208    681
  Planarity :  0.006   0.111    756
  Dihedral  : 15.188  81.808   1389
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.34 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.17 %
    Favored  : 82.91 %
  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: -3.71 (0.29), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.89 (0.41), residues: 135
  loop : -2.90 (0.24), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  35 
 TYR   0.021   0.001   TYR E 112 
 PHE   0.023   0.001   PHE D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4083)
  covalent geometry    : angle       0.79664 ( 5583)
  hydrogen bonds       : bond        0.24827 (   89)
  hydrogen bonds       : angle      10.49536 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.5638 (tmm-80) cc_final: 0.3355 (ptp90)
REVERT: C  100 ILE cc_start: 0.8295 (mt) cc_final: 0.7982 (mm)
REVERT: D  137 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7466 (p0)
REVERT: E  166 SER cc_start: 0.8191 (t) cc_final: 0.7642 (m)
REVERT: E  197 PRO cc_start: 0.6214 (Cg_endo) cc_final: 0.6010 (Cg_endo)
REVERT: E  215 VAL cc_start: 0.7761 (m) cc_final: 0.7529 (p)
  outliers start: 9
  outliers final: 2
  residues processed: 66
  average time/residue: 0.0541
  time to fit residues: 4.6904
Evaluate side-chains
  50 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C 106 ASN
E 156 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.076548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.073099 restraints weight = 17453.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.074159 restraints weight = 10425.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.074847 restraints weight = 6579.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.075334 restraints weight = 4376.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.075698 restraints weight = 2973.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   4083  Z= 0.169
  Angle     :  0.781   7.560   5583  Z= 0.435
  Chirality :  0.052   0.173    681
  Planarity :  0.004   0.040    756
  Dihedral  :  7.592  24.217    585
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.98 %
    Favored  : 86.02 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.13 %
    Favored  : 94.66 %
  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: -3.56 (0.29), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.24 (0.43), residues: 123
  loop : -2.98 (0.24), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E  35 
 TYR   0.014   0.002   TYR D 128 
 PHE   0.026   0.002   PHE D  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 4083)
  covalent geometry    : angle       0.78109 ( 5583)
  hydrogen bonds       : bond        0.04607 (   89)
  hydrogen bonds       : angle       7.44771 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6124 (tmm-80) cc_final: 0.3933 (ptp90)
REVERT: D   35 ARG cc_start: 0.7317 (mmt90) cc_final: 0.6876 (mmt180)
REVERT: D  127 SER cc_start: 0.7818 (p) cc_final: 0.7553 (p)
REVERT: E  166 SER cc_start: 0.7710 (t) cc_final: 0.7280 (p)
REVERT: E  215 VAL cc_start: 0.7922 (m) cc_final: 0.7497 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0570
  time to fit residues: 4.6466
Evaluate side-chains
  47 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0570
   chunk 5 optimal weight:    0.0980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5100

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.078362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.074799 restraints weight = 17759.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.075858 restraints weight = 10657.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.076594 restraints weight = 6834.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.077083 restraints weight = 4531.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.077418 restraints weight = 3102.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4083  Z= 0.131
  Angle     :  0.694   5.907   5583  Z= 0.388
  Chirality :  0.049   0.171    681
  Planarity :  0.004   0.042    756
  Dihedral  :  7.033  25.633    585
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.65 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  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: -3.34 (0.30), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.49 (0.41), residues: 150
  loop : -2.71 (0.25), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  35 
 TYR   0.013   0.002   TYR D 128 
 PHE   0.010   0.001   PHE D  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4083)
  covalent geometry    : angle       0.69403 ( 5583)
  hydrogen bonds       : bond        0.03630 (   89)
  hydrogen bonds       : angle       6.71337 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6114 (tmm-80) cc_final: 0.4005 (ptp90)
REVERT: D   35 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6595 (mmt180)
REVERT: E  215 VAL cc_start: 0.8018 (m) cc_final: 0.7581 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0514
  time to fit residues: 4.1558
Evaluate side-chains
  47 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
C  86 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.072057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.068388 restraints weight = 18216.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.069561 restraints weight = 10230.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.070340 restraints weight = 6209.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.070856 restraints weight = 3958.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.071200 restraints weight = 2602.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   4083  Z= 0.277
  Angle     :  0.934   7.343   5583  Z= 0.521
  Chirality :  0.057   0.198    681
  Planarity :  0.005   0.041    756
  Dihedral  :  8.835  28.630    585
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.59 %
    Favored  : 84.41 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.98 %
    Favored  : 93.80 %
  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: -3.80 (0.29), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.84 (0.40), residues: 156
  loop : -3.04 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  35 
 TYR   0.014   0.002   TYR E 112 
 PHE   0.024   0.003   PHE E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 4083)
  covalent geometry    : angle       0.93415 ( 5583)
  hydrogen bonds       : bond        0.04464 (   89)
  hydrogen bonds       : angle       7.72955 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6316 (tmm-80) cc_final: 0.5766 (ttp-110)
REVERT: D   35 ARG cc_start: 0.7438 (mmt90) cc_final: 0.7044 (mmt180)
REVERT: E  127 SER cc_start: 0.8099 (p) cc_final: 0.7883 (p)
REVERT: E  215 VAL cc_start: 0.8235 (m) cc_final: 0.7813 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0500
  time to fit residues: 3.8927
Evaluate side-chains
  41 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0070
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0670
   chunk 34 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
C  86 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.077234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.073316 restraints weight = 17634.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.074562 restraints weight = 9923.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.075360 restraints weight = 6058.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.075916 restraints weight = 3909.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.076298 restraints weight = 2605.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4083  Z= 0.136
  Angle     :  0.714   7.866   5583  Z= 0.398
  Chirality :  0.050   0.172    681
  Planarity :  0.004   0.043    756
  Dihedral  :  7.421  26.256    585
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.65 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  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: -3.63 (0.30), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.86 (0.40), residues: 162
  loop : -2.86 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  98 
 TYR   0.014   0.002   TYR C 112 
 PHE   0.013   0.002   PHE E  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4083)
  covalent geometry    : angle       0.71404 ( 5583)
  hydrogen bonds       : bond        0.03262 (   89)
  hydrogen bonds       : angle       6.60120 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6636 (tmm-80) cc_final: 0.4239 (ptp90)
REVERT: D   35 ARG cc_start: 0.7296 (mmt90) cc_final: 0.6536 (mmt180)
REVERT: E  215 VAL cc_start: 0.8220 (m) cc_final: 0.7749 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0566
  time to fit residues: 4.0696
Evaluate side-chains
  34 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0040
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.9794

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.076095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.072352 restraints weight = 17929.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.073555 restraints weight = 10384.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.074345 restraints weight = 6411.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.074858 restraints weight = 4132.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.075223 restraints weight = 2778.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4083  Z= 0.159
  Angle     :  0.740   6.347   5583  Z= 0.410
  Chirality :  0.051   0.169    681
  Planarity :  0.004   0.041    756
  Dihedral  :  7.374  25.441    585
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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: -3.60 (0.31), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.75 (0.41), residues: 162
  loop : -2.88 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  35 
 TYR   0.011   0.002   TYR E 112 
 PHE   0.021   0.002   PHE E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4083)
  covalent geometry    : angle       0.73964 ( 5583)
  hydrogen bonds       : bond        0.03425 (   89)
  hydrogen bonds       : angle       6.37804 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6730 (tmm-80) cc_final: 0.4301 (ptp90)
REVERT: D   35 ARG cc_start: 0.7330 (mmt90) cc_final: 0.6712 (mmt180)
REVERT: E  215 VAL cc_start: 0.8213 (m) cc_final: 0.7776 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0635
  time to fit residues: 4.1593
Evaluate side-chains
  35 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.0370
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7260

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.077120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.073553 restraints weight = 17745.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.074651 restraints weight = 10322.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075370 restraints weight = 6412.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.075867 restraints weight = 4203.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.076220 restraints weight = 2856.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4083  Z= 0.138
  Angle     :  0.704   7.718   5583  Z= 0.388
  Chirality :  0.049   0.171    681
  Planarity :  0.004   0.039    756
  Dihedral  :  7.030  24.767    585
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.72 %
    Favored  : 87.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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: -3.51 (0.31), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.57 (0.42), residues: 162
  loop : -2.87 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  35 
 TYR   0.011   0.001   TYR C 112 
 PHE   0.018   0.002   PHE E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4083)
  covalent geometry    : angle       0.70407 ( 5583)
  hydrogen bonds       : bond        0.03267 (   89)
  hydrogen bonds       : angle       6.04231 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6552 (tmm-80) cc_final: 0.4315 (ptp90)
REVERT: D   35 ARG cc_start: 0.7157 (mmt90) cc_final: 0.6471 (mmt180)
REVERT: E  112 TYR cc_start: 0.8065 (p90) cc_final: 0.7830 (p90)
REVERT: E  215 VAL cc_start: 0.8219 (m) cc_final: 0.7774 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0592
  time to fit residues: 4.2963
Evaluate side-chains
  37 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 47 optimal weight:    0.1980
   chunk 28 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.5540

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.077688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.074211 restraints weight = 17450.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.075291 restraints weight = 10186.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.075994 restraints weight = 6346.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.076480 restraints weight = 4172.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.076819 restraints weight = 2842.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4083  Z= 0.136
  Angle     :  0.702   7.541   5583  Z= 0.385
  Chirality :  0.050   0.178    681
  Planarity :  0.004   0.041    756
  Dihedral  :  6.794  24.828    585
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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: -3.43 (0.31), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.61 (0.42), residues: 168
  loop : -2.78 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  35 
 TYR   0.011   0.002   TYR C 148 
 PHE   0.017   0.002   PHE E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4083)
  covalent geometry    : angle       0.70162 ( 5583)
  hydrogen bonds       : bond        0.03522 (   89)
  hydrogen bonds       : angle       5.97322 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6503 (tmm-80) cc_final: 0.4313 (ptp90)
REVERT: D   35 ARG cc_start: 0.6935 (mmt90) cc_final: 0.6270 (mmt180)
REVERT: E  112 TYR cc_start: 0.7982 (p90) cc_final: 0.7740 (p90)
REVERT: E  215 VAL cc_start: 0.8224 (m) cc_final: 0.7794 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0668
  time to fit residues: 4.6609
Evaluate side-chains
  39 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 43 optimal weight:    0.3980
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.074216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.070572 restraints weight = 18450.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.071748 restraints weight = 10520.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.072479 restraints weight = 6462.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.073002 restraints weight = 4191.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.073289 restraints weight = 2812.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4083  Z= 0.209
  Angle     :  0.799   6.591   5583  Z= 0.441
  Chirality :  0.053   0.166    681
  Planarity :  0.004   0.035    756
  Dihedral  :  7.638  24.064    585
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.77 %
    Favored  : 84.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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 (0.30), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.22 (0.52), residues: 111
  loop : -3.06 (0.23), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  35 
 TYR   0.012   0.002   TYR C 148 
 PHE   0.022   0.003   PHE E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 4083)
  covalent geometry    : angle       0.79904 ( 5583)
  hydrogen bonds       : bond        0.03836 (   89)
  hydrogen bonds       : angle       6.61714 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6295 (tmm-80) cc_final: 0.4273 (ptp90)
REVERT: D   35 ARG cc_start: 0.7151 (mmt90) cc_final: 0.6673 (mmt180)
REVERT: E  215 VAL cc_start: 0.8427 (m) cc_final: 0.8001 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0668
  time to fit residues: 4.2144
Evaluate side-chains
  36 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.4980
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.073404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.069676 restraints weight = 18221.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.070880 restraints weight = 10351.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.071643 restraints weight = 6302.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.072154 restraints weight = 4056.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.072525 restraints weight = 2714.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4083  Z= 0.214
  Angle     :  0.812   7.087   5583  Z= 0.450
  Chirality :  0.054   0.192    681
  Planarity :  0.004   0.033    756
  Dihedral  :  7.932  24.921    585
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.77 %
    Favored  : 84.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.75 (0.29), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.34 (0.52), residues: 111
  loop : -3.10 (0.23), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  35 
 TYR   0.012   0.002   TYR C 148 
 PHE   0.022   0.002   PHE E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 4083)
  covalent geometry    : angle       0.81214 ( 5583)
  hydrogen bonds       : bond        0.04005 (   89)
  hydrogen bonds       : angle       6.80664 (  219)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.6359 (tmm-80) cc_final: 0.4271 (ptp90)
REVERT: D   35 ARG cc_start: 0.7132 (mmt90) cc_final: 0.6674 (mmt180)
REVERT: D  117 THR cc_start: 0.8389 (p) cc_final: 0.8004 (p)
REVERT: E  215 VAL cc_start: 0.8542 (m) cc_final: 0.8094 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0663
  time to fit residues: 4.2589
Evaluate side-chains
  39 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.073941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.070478 restraints weight = 18166.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.071576 restraints weight = 10471.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.072280 restraints weight = 6479.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.072781 restraints weight = 4237.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.073122 restraints weight = 2838.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4083  Z= 0.191
  Angle     :  0.772   6.086   5583  Z= 0.430
  Chirality :  0.052   0.177    681
  Planarity :  0.004   0.037    756
  Dihedral  :  7.756  24.878    585
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.95 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.78 (0.29), residues: 558
  helix:  None (None), residues: 0
  sheet: -1.38 (0.52), residues: 111
  loop : -3.12 (0.23), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  35 
 TYR   0.011   0.002   TYR C 148 
 PHE   0.016   0.002   PHE E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4083)
  covalent geometry    : angle       0.77201 ( 5583)
  hydrogen bonds       : bond        0.03975 (   89)
  hydrogen bonds       : angle       6.70850 (  219)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 795.44 seconds
wall clock time: 14 minutes 31.49 seconds (871.49 seconds total)