Starting phenix.real_space_refine
on Tue Mar  3 10:59:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4d_31708/03_2026/7v4d_31708.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4d_31708/03_2026/7v4d_31708.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2026/7v4d_31708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2026/7v4d_31708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2026/7v4d_31708.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2026/7v4d_31708.cif"
  }
  resolution = 3.5
  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=   0.002
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    1488      2.51       5
     N     408      2.21       5
     O     480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 2376
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 396
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
  Restraints were copied for chains:
    C, D, E, A, B
  Time building chain proxies: 0.41, per 1000 atoms: 0.17
  Number of scatterers: 2376
  At special positions: 0
  Unit cell: (98.58, 87.98, 31.8, 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     480      8.00
     N     408      7.00
     C    1488      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: 0.17
  Conformation dependent library (CDL) restraints added in 102.2 milliseconds
  

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  588

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 44
      removed outlier: 6.367A  pdb=" N   LYS F  43 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   LYS C  43 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 50
    Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 55
    Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63
      removed outlier: 6.128A  pdb=" N   GLN F  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   GLN C  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 70 through 71
    Processing sheet with id=AA6, first strand: chain 'F' and resid 81 through 82
    Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 44
      removed outlier: 6.361A  pdb=" N   LYS E  43 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LYS A  43 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50
    Processing sheet with id=AA9, first strand: chain 'E' and resid 54 through 55
    Processing sheet with id=AB1, first strand: chain 'E' and resid 62 through 63
      removed outlier: 6.129A  pdb=" N   GLN E  62 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   GLN A  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 71
    Processing sheet with id=AB3, first strand: chain 'E' and resid 81 through 82

    20 hydrogen bonds defined for protein.
    60 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: 0.30

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 414
        1.29 -     1.35: 373
        1.35 -     1.42: 102
        1.42 -     1.48: 401
        1.48 -     1.55: 1098
  Bond restraints: 2388
  Sorted by residual:
  bond pdb=" CA  LEU D  38 "
       pdb=" C   LEU D  38 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.011 1.10e-02 8.26e+03 9.42e-01
  bond pdb=" CA  LEU F  38 "
       pdb=" C   LEU F  38 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.011 1.10e-02 8.26e+03 9.17e-01
  bond pdb=" CA  LEU A  38 "
       pdb=" C   LEU A  38 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.10e-02 8.26e+03 9.07e-01
  bond pdb=" CA  LEU E  38 "
       pdb=" C   LEU E  38 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.10e-02 8.26e+03 9.04e-01
  bond pdb=" CA  LEU C  38 "
       pdb=" C   LEU C  38 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.10e-02 8.26e+03 8.62e-01
  ... (remaining 2383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.68: 2731
        0.68 -     1.36: 401
        1.36 -     2.04: 84
        2.04 -     2.72: 18
        2.72 -     3.41: 6
  Bond angle restraints: 3240
  Sorted by residual:
  angle pdb=" CA  ASN B  65 "
        pdb=" CB  ASN B  65 "
        pdb=" CG  ASN B  65 "
      ideal   model   delta    sigma   weight residual
     112.60  114.52   -1.92 1.00e+00 1.00e+00 3.70e+00
  angle pdb=" CA  ASN A  65 "
        pdb=" CB  ASN A  65 "
        pdb=" CG  ASN A  65 "
      ideal   model   delta    sigma   weight residual
     112.60  114.49   -1.89 1.00e+00 1.00e+00 3.58e+00
  angle pdb=" CA  ASN E  65 "
        pdb=" CB  ASN E  65 "
        pdb=" CG  ASN E  65 "
      ideal   model   delta    sigma   weight residual
     112.60  114.49   -1.89 1.00e+00 1.00e+00 3.58e+00
  angle pdb=" CA  ASN C  65 "
        pdb=" CB  ASN C  65 "
        pdb=" CG  ASN C  65 "
      ideal   model   delta    sigma   weight residual
     112.60  114.48   -1.88 1.00e+00 1.00e+00 3.54e+00
  angle pdb=" CA  ASN F  65 "
        pdb=" CB  ASN F  65 "
        pdb=" CG  ASN F  65 "
      ideal   model   delta    sigma   weight residual
     112.60  114.48   -1.88 1.00e+00 1.00e+00 3.52e+00
  ... (remaining 3235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.21: 1206
       12.21 -    24.43: 132
       24.43 -    36.64: 18
       36.64 -    48.85: 12
       48.85 -    61.07: 6
  Dihedral angle restraints: 1374
    sinusoidal: 438
      harmonic: 936
  Sorted by residual:
  dihedral pdb=" CA  VAL A  48 "
           pdb=" C   VAL A  48 "
           pdb=" N   VAL A  49 "
           pdb=" CA  VAL A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.67   17.33     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  VAL B  48 "
           pdb=" C   VAL B  48 "
           pdb=" N   VAL B  49 "
           pdb=" CA  VAL B  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  VAL C  48 "
           pdb=" C   VAL C  48 "
           pdb=" N   VAL C  49 "
           pdb=" CA  VAL C  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.71   17.29     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 1371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 214
       0.025 -    0.049: 108
       0.049 -    0.074: 52
       0.074 -    0.099: 34
       0.099 -    0.124: 24
  Chirality restraints: 432
  Sorted by residual:
  chirality pdb=" CA  VAL A  70 "
            pdb=" N   VAL A  70 "
            pdb=" C   VAL A  70 "
            pdb=" CB  VAL A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  chirality pdb=" CA  VAL D  70 "
            pdb=" N   VAL D  70 "
            pdb=" C   VAL D  70 "
            pdb=" CB  VAL D  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  VAL C  70 "
            pdb=" N   VAL C  70 "
            pdb=" C   VAL C  70 "
            pdb=" CB  VAL C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 429 not shown)

  Planarity restraints: 402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C  87 "    0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   SER C  87 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   SER C  87 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE C  88 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E  87 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.29e+00
        pdb=" C   SER E  87 "    0.020 2.00e-02 2.50e+03
        pdb=" O   SER E  87 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ILE E  88 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F  87 "    0.006 2.00e-02 2.50e+03   1.12e-02 1.25e+00
        pdb=" C   SER F  87 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   SER F  87 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE F  88 "    0.006 2.00e-02 2.50e+03
  ... (remaining 399 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 331
        2.77 -     3.30: 2209
        3.30 -     3.83: 3524
        3.83 -     4.37: 3821
        4.37 -     4.90: 7885
  Nonbonded interactions: 17770
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  61 "
            pdb=" OG1 THR A  72 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE1 GLU E  61 "
            pdb=" OG1 THR E  72 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OE1 GLU C  61 "
            pdb=" OG1 THR C  72 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OE1 GLU B  61 "
            pdb=" OG1 THR B  72 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OE1 GLU F  61 "
            pdb=" OG1 THR F  72 "
     model   vdw
     2.235 3.040
  ... (remaining 17765 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 'F'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'A'
  selection = chain 'B'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
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      :  0.003   0.024   2388  Z= 0.143
  Angle     :  0.544   3.405   3240  Z= 0.315
  Chirality :  0.045   0.124    432
  Planarity :  0.002   0.011    402
  Dihedral  : 11.888  61.066    786
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  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 are not related in a simple way.
  whole: -5.68 (0.26), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.32 (0.20), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR B  39 
 PHE   0.001   0.000   PHE F  94 
 HIS   0.001   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2388)
  covalent geometry    : angle       0.54444 ( 3240)
  hydrogen bonds       : bond        0.11578 (   20)
  hydrogen bonds       : angle       7.71212 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.079 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7834 (pm20)
REVERT: C   46 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8023 (mt-10)
REVERT: C   83 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7843 (mm-30)
REVERT: B   62 GLN cc_start: 0.8139 (tt0) cc_final: 0.7757 (tt0)
REVERT: B   83 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7599 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0307
  time to fit residues: 1.7048
Evaluate side-chains
  35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 = 0.4398 r_free = 0.4398 target = 0.161202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.132484 restraints weight = 2788.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.135886 restraints weight = 1424.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.138269 restraints weight = 980.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.139758 restraints weight = 782.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.140033 restraints weight = 683.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   2388  Z= 0.301
  Angle     :  0.711   5.437   3240  Z= 0.389
  Chirality :  0.048   0.138    432
  Planarity :  0.003   0.016    402
  Dihedral  :  5.795  16.206    348
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.10 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 13.33 %
    Favored  : 77.92 %
  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 are not related in a simple way.
  whole: -5.51 (0.29), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.20 (0.22), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR B  39 
 PHE   0.007   0.001   PHE D  94 
 HIS   0.001   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00686 ( 2388)
  covalent geometry    : angle       0.71103 ( 3240)
  hydrogen bonds       : bond        0.05157 (   20)
  hydrogen bonds       : angle       6.05113 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 41
  time to evaluate  : 0.062 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7661 (pm20)
REVERT: C   46 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7954 (mt-10)
REVERT: C   83 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7981 (mm-30)
REVERT: B   62 GLN cc_start: 0.8239 (tt0) cc_final: 0.7865 (tt0)
REVERT: B   83 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7632 (mm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 56
  average time/residue: 0.0273
  time to fit residues: 2.1323
Evaluate side-chains
  54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   71 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.174262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.145827 restraints weight = 2581.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.149488 restraints weight = 1264.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.151896 restraints weight = 845.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.153263 restraints weight = 672.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.154159 restraints weight = 587.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2388  Z= 0.120
  Angle     :  0.545   4.183   3240  Z= 0.304
  Chirality :  0.047   0.130    432
  Planarity :  0.002   0.014    402
  Dihedral  :  4.969  16.533    348
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 19.58 %
    Favored  : 73.75 %
  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 are not related in a simple way.
  whole: -4.93 (0.32), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.24), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR C  39 
 PHE   0.002   0.000   PHE D  94 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2388)
  covalent geometry    : angle       0.54524 ( 3240)
  hydrogen bonds       : bond        0.04245 (   20)
  hydrogen bonds       : angle       5.56389 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.091 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7680 (pm20)
REVERT: C   46 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7903 (mt-10)
REVERT: C   83 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7893 (mm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 50
  average time/residue: 0.0271
  time to fit residues: 1.9207
Evaluate side-chains
  49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 27 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
F  50 HIS
E  50 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.162741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.133850 restraints weight = 2728.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.137062 restraints weight = 1438.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.139139 restraints weight = 1008.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.140750 restraints weight = 822.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.141290 restraints weight = 717.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   2388  Z= 0.296
  Angle     :  0.711   5.572   3240  Z= 0.389
  Chirality :  0.048   0.217    432
  Planarity :  0.003   0.015    402
  Dihedral  :  5.674  16.565    348
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.31 %
    Favored  : 88.69 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 14.58 %
    Favored  : 75.00 %
  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 are not related in a simple way.
  whole: -4.99 (0.32), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.25), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR B  39 
 PHE   0.006   0.001   PHE D  94 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00681 ( 2388)
  covalent geometry    : angle       0.71052 ( 3240)
  hydrogen bonds       : bond        0.05368 (   20)
  hydrogen bonds       : angle       5.90690 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.066 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7716 (pm20)
REVERT: C   46 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8038 (mt-10)
REVERT: C   83 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7924 (mm-30)
REVERT: D   83 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7730 (mm-30)
REVERT: B   62 GLN cc_start: 0.8240 (tt0) cc_final: 0.7871 (tt0)
  outliers start: 25
  outliers final: 23
  residues processed: 54
  average time/residue: 0.0197
  time to fit residues: 1.4977
Evaluate side-chains
  61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 38
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   88 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 28 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.4560 r_free = 0.4560 target = 0.167933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.140931 restraints weight = 2645.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.144354 restraints weight = 1389.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.146194 restraints weight = 944.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.147715 restraints weight = 771.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.148669 restraints weight = 666.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2388  Z= 0.145
  Angle     :  0.602   4.943   3240  Z= 0.334
  Chirality :  0.048   0.175    432
  Planarity :  0.002   0.013    402
  Dihedral  :  5.100  15.845    348
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers : 10.83 %
    Allowed  : 14.17 %
    Favored  : 75.00 %
  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 are not related in a simple way.
  whole: -4.57 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR B  39 
 PHE   0.003   0.001   PHE D  94 
 HIS   0.001   0.000   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 2388)
  covalent geometry    : angle       0.60210 ( 3240)
  hydrogen bonds       : bond        0.04632 (   20)
  hydrogen bonds       : angle       5.79138 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 37
  time to evaluate  : 0.076 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7777 (pm20)
REVERT: C   46 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7929 (mt-10)
REVERT: C   83 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7864 (mm-30)
REVERT: A   79 GLN cc_start: 0.8552 (mt0) cc_final: 0.8192 (mt0)
  outliers start: 26
  outliers final: 21
  residues processed: 55
  average time/residue: 0.0213
  time to fit residues: 1.6744
Evaluate side-chains
  57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 36
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   88 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.4488 r_free = 0.4488 target = 0.163679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.136525 restraints weight = 2717.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.139721 restraints weight = 1462.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.141828 restraints weight = 1024.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.143169 restraints weight = 828.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.144067 restraints weight = 721.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   2388  Z= 0.265
  Angle     :  0.702   6.776   3240  Z= 0.381
  Chirality :  0.048   0.155    432
  Planarity :  0.003   0.014    402
  Dihedral  :  5.523  16.054    348
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers : 11.67 %
    Allowed  : 14.17 %
    Favored  : 74.17 %
  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 are not related in a simple way.
  whole: -4.59 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR B  39 
 PHE   0.006   0.001   PHE D  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 2388)
  covalent geometry    : angle       0.70174 ( 3240)
  hydrogen bonds       : bond        0.04610 (   20)
  hydrogen bonds       : angle       5.74453 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 34
  time to evaluate  : 0.082 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7781 (pm20)
REVERT: C   46 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8020 (mt-10)
  outliers start: 28
  outliers final: 23
  residues processed: 54
  average time/residue: 0.0222
  time to fit residues: 1.7087
Evaluate side-chains
  57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 34
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   88 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.4547 r_free = 0.4547 target = 0.167162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.140070 restraints weight = 2660.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.143393 restraints weight = 1384.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.145513 restraints weight = 955.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.146850 restraints weight = 768.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.147625 restraints weight = 672.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2388  Z= 0.184
  Angle     :  0.673   7.537   3240  Z= 0.365
  Chirality :  0.048   0.158    432
  Planarity :  0.003   0.020    402
  Dihedral  :  5.221  15.960    348
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers : 11.25 %
    Allowed  : 15.00 %
    Favored  : 73.75 %
  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 are not related in a simple way.
  whole: -4.33 (0.35), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.27), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  39 
 PHE   0.004   0.001   PHE D  94 
 HIS   0.001   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2388)
  covalent geometry    : angle       0.67306 ( 3240)
  hydrogen bonds       : bond        0.04346 (   20)
  hydrogen bonds       : angle       5.58331 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 34
  time to evaluate  : 0.086 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7763 (pm20)
REVERT: C   46 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7967 (mt-10)
  outliers start: 27
  outliers final: 23
  residues processed: 54
  average time/residue: 0.0195
  time to fit residues: 1.5272
Evaluate side-chains
  57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 34
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   88 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 17 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    0.1980
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.4720 r_free = 0.4720 target = 0.184590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.156872 restraints weight = 2493.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.160137 restraints weight = 1316.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.162354 restraints weight = 919.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.163861 restraints weight = 741.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.164569 restraints weight = 648.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2388  Z= 0.098
  Angle     :  0.563   7.737   3240  Z= 0.301
  Chirality :  0.048   0.161    432
  Planarity :  0.003   0.020    402
  Dihedral  :  4.470  16.133    348
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  7.92 %
    Allowed  : 17.50 %
    Favored  : 74.58 %
  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 are not related in a simple way.
  whole: -3.90 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR B  39 
 PHE   0.002   0.001   PHE D  94 
 HIS   0.001   0.000   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 2388)
  covalent geometry    : angle       0.56262 ( 3240)
  hydrogen bonds       : bond        0.04057 (   20)
  hydrogen bonds       : angle       5.32199 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 32
  time to evaluate  : 0.062 
Fit side-chains
REVERT: C   46 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7820 (mt-10)
  outliers start: 19
  outliers final: 14
  residues processed: 49
  average time/residue: 0.0256
  time to fit residues: 1.7800
Evaluate side-chains
  45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    0.2980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4643 r_free = 0.4643 target = 0.175026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.147885 restraints weight = 2652.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.151193 restraints weight = 1355.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.153428 restraints weight = 931.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.154500 restraints weight = 745.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.155544 restraints weight = 663.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2388  Z= 0.126
  Angle     :  0.585   7.696   3240  Z= 0.310
  Chirality :  0.047   0.128    432
  Planarity :  0.003   0.021    402
  Dihedral  :  4.522  16.303    348
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 17.50 %
    Favored  : 75.42 %
  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 are not related in a simple way.
  whole: -3.67 (0.38), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR A  39 
 PHE   0.003   0.001   PHE D  94 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 2388)
  covalent geometry    : angle       0.58507 ( 3240)
  hydrogen bonds       : bond        0.03648 (   20)
  hydrogen bonds       : angle       5.35018 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.090 
Fit side-chains
REVERT: C   46 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7807 (mt-10)
  outliers start: 17
  outliers final: 15
  residues processed: 47
  average time/residue: 0.0291
  time to fit residues: 1.9334
Evaluate side-chains
  49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0040
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9996

-------------------------------------------------------------------------------
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 = 0.4637 r_free = 0.4637 target = 0.173927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.147048 restraints weight = 2691.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.150408 restraints weight = 1382.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.152584 restraints weight = 937.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.153934 restraints weight = 745.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.154556 restraints weight = 650.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2388  Z= 0.134
  Angle     :  0.596   8.282   3240  Z= 0.314
  Chirality :  0.046   0.128    432
  Planarity :  0.003   0.020    402
  Dihedral  :  4.606  16.063    348
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 17.50 %
    Favored  : 75.83 %
  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 are not related in a simple way.
  whole: -3.58 (0.38), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR A  39 
 PHE   0.003   0.001   PHE C  94 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 2388)
  covalent geometry    : angle       0.59625 ( 3240)
  hydrogen bonds       : bond        0.03468 (   20)
  hydrogen bonds       : angle       5.31964 (   60)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 32
  time to evaluate  : 0.081 
Fit side-chains
REVERT: C   46 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7884 (mt-10)
  outliers start: 16
  outliers final: 15
  residues processed: 45
  average time/residue: 0.0273
  time to fit residues: 1.7394
Evaluate side-chains
  47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.4616 r_free = 0.4616 target = 0.171592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.144432 restraints weight = 2684.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.147896 restraints weight = 1347.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.150093 restraints weight = 913.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.151329 restraints weight = 730.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.152257 restraints weight = 641.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2388  Z= 0.153
  Angle     :  0.611   8.158   3240  Z= 0.323
  Chirality :  0.046   0.129    432
  Planarity :  0.003   0.019    402
  Dihedral  :  4.765  16.479    348
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 17.92 %
    Favored  : 75.83 %
  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 are not related in a simple way.
  whole: -3.55 (0.38), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR F  39 
 PHE   0.003   0.001   PHE D  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2388)
  covalent geometry    : angle       0.61107 ( 3240)
  hydrogen bonds       : bond        0.03602 (   20)
  hydrogen bonds       : angle       5.62687 (   60)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 562.31 seconds
wall clock time: 10 minutes 23.79 seconds (623.79 seconds total)