Starting phenix.real_space_refine
on Wed Jul  1 22:38:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mek_48216/07_2026/9mek_48216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mek_48216/07_2026/9mek_48216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mek_48216/07_2026/9mek_48216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mek_48216/07_2026/9mek_48216.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mek_48216/07_2026/9mek_48216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mek_48216/07_2026/9mek_48216.map"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.062
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: 5
    Type Number    sf(0)   Gaussians
     K       4      8.98       5
     S      12      5.16       5
     C    2396      2.51       5
     N     576      2.21       5
     O     606      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-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3594
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1788
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "B"
      Number of atoms: 1788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1788
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 7
          Ad-hoc single atom residues: {'  K': 4}
          Unusual residues: {'HP6': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'HP6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.12, per 1000 atoms: 0.31
  Number of scatterers: 3594
  At special positions: 0
  Unit cell: (71.775, 61.625, 89.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       4     19.00
     S      12     16.00
     O     606      8.00
     N     576      7.00
     C    2396      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS B  53 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 129.8 milliseconds
  

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  892

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      77.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 51
      Proline residue:  A  31  - end of helix
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 72 through 78
      removed outlier: 3.796A  pdb=" N   VAL A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 116 through 151
      Proline residue:  A 132  - end of helix
      removed outlier: 3.592A  pdb=" N   HIS A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 195
      removed outlier: 3.608A  pdb=" N   TRP A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 200 through 213
    Processing helix  chain 'A' and resid 230 through 264
    Processing helix  chain 'A' and resid 267 through 271
    Processing helix  chain 'B' and resid 8 through 51
      Proline residue:  B  31  - end of helix
    Processing helix  chain 'B' and resid 55 through 69
    Processing helix  chain 'B' and resid 72 through 78
      removed outlier: 3.796A  pdb=" N   VAL B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 105
    Processing helix  chain 'B' and resid 116 through 151
      Proline residue:  B 132  - end of helix
      removed outlier: 3.592A  pdb=" N   HIS B 151 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 213
    Processing helix  chain 'B' and resid 230 through 264
    Processing helix  chain 'B' and resid 267 through 271

    280 hydrogen bonds defined for protein.
    840 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: 0.55

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1096
        1.34 -     1.46: 832
        1.46 -     1.58: 1726
        1.58 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3670
  Sorted by residual:
  bond pdb=" CA  PRO A 226 "
       pdb=" C   PRO A 226 "
    ideal  model  delta    sigma   weight residual
    1.527  1.520  0.007 1.07e-02 8.73e+03 4.60e-01
  bond pdb=" CA  PRO B 226 "
       pdb=" C   PRO B 226 "
    ideal  model  delta    sigma   weight residual
    1.527  1.520  0.007 1.07e-02 8.73e+03 4.60e-01
  bond pdb=" CA  PRO B 226 "
       pdb=" CB  PRO B 226 "
    ideal  model  delta    sigma   weight residual
    1.530  1.537 -0.006 1.03e-02 9.43e+03 3.64e-01
  bond pdb=" CA  PRO A 226 "
       pdb=" CB  PRO A 226 "
    ideal  model  delta    sigma   weight residual
    1.530  1.537 -0.006 1.03e-02 9.43e+03 3.64e-01
  bond pdb=" N   PRO A 226 "
       pdb=" CA  PRO A 226 "
    ideal  model  delta    sigma   weight residual
    1.479  1.470  0.010 1.71e-02 3.42e+03 3.24e-01
  ... (remaining 3665 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 4780
        1.01 -     2.02: 176
        2.02 -     3.03: 44
        3.03 -     4.05: 6
        4.05 -     5.06: 14
  Bond angle restraints: 5020
  Sorted by residual:
  angle pdb=" N   PHE A 185 "
        pdb=" CA  PHE A 185 "
        pdb=" C   PHE A 185 "
      ideal   model   delta    sigma   weight residual
     114.75  110.69    4.06 1.26e+00 6.30e-01 1.04e+01
  angle pdb=" N   PHE B 185 "
        pdb=" CA  PHE B 185 "
        pdb=" C   PHE B 185 "
      ideal   model   delta    sigma   weight residual
     114.75  110.69    4.06 1.26e+00 6.30e-01 1.04e+01
  angle pdb=" CA  PHE B 185 "
        pdb=" C   PHE B 185 "
        pdb=" N   LEU B 186 "
      ideal   model   delta    sigma   weight residual
     119.80  117.04    2.76 1.34e+00 5.57e-01 4.25e+00
  angle pdb=" CA  PHE A 185 "
        pdb=" C   PHE A 185 "
        pdb=" N   LEU A 186 "
      ideal   model   delta    sigma   weight residual
     119.80  117.04    2.76 1.34e+00 5.57e-01 4.25e+00
  angle pdb=" N   GLY B 130 "
        pdb=" CA  GLY B 130 "
        pdb=" C   GLY B 130 "
      ideal   model   delta    sigma   weight residual
     113.18  117.61   -4.43 2.37e+00 1.78e-01 3.49e+00
  ... (remaining 5015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.48: 1758
       12.48 -    24.97: 221
       24.97 -    37.45: 98
       37.45 -    49.93: 26
       49.93 -    62.41: 6
  Dihedral angle restraints: 2109
    sinusoidal: 727
      harmonic: 1382
  Sorted by residual:
  dihedral pdb=" CB  ARG A  27 "
           pdb=" CG  ARG A  27 "
           pdb=" CD  ARG A  27 "
           pdb=" NE  ARG A  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.27  -52.73     3      1.50e+01 4.44e-03 9.14e+00
  dihedral pdb=" CB  ARG B  27 "
           pdb=" CG  ARG B  27 "
           pdb=" CD  ARG B  27 "
           pdb=" NE  ARG B  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.27  -52.73     3      1.50e+01 4.44e-03 9.14e+00
  dihedral pdb=" N   LEU A  43 "
           pdb=" CA  LEU A  43 "
           pdb=" CB  LEU A  43 "
           pdb=" CG  LEU A  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -129.61  -50.39     3      1.50e+01 4.44e-03 8.89e+00
  ... (remaining 2106 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 398
       0.025 -    0.049: 146
       0.049 -    0.073: 62
       0.073 -    0.098: 14
       0.098 -    0.122: 14
  Chirality restraints: 634
  Sorted by residual:
  chirality pdb=" CB  THR A  42 "
            pdb=" CA  THR A  42 "
            pdb=" OG1 THR A  42 "
            pdb=" CG2 THR A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.43    0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CB  THR B  42 "
            pdb=" CA  THR B  42 "
            pdb=" OG1 THR B  42 "
            pdb=" CG2 THR B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.43    0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CA  THR B 106 "
            pdb=" N   THR B 106 "
            pdb=" C   THR B 106 "
            pdb=" CB  THR B 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.41    0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 631 not shown)

  Planarity restraints: 606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 225 "   -0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A 226 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 226 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 226 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 225 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO B 226 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B 226 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 226 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 181 "   -0.005 2.00e-02 2.50e+03   1.06e-02 1.12e+00
        pdb=" C   VAL B 181 "    0.018 2.00e-02 2.50e+03
        pdb=" O   VAL B 181 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   THR B 182 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 603 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.87: 1335
        2.87 -     3.44: 4354
        3.44 -     4.01: 6694
        4.01 -     4.57: 9960
        4.57 -     5.14: 13224
  Nonbonded interactions: 35567
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 209 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   PHE B 209 "
            pdb=" OG  SER B 213 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OE2 GLU A  29 "
            pdb=" N   LEU B 115 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" N   LEU A 115 "
            pdb=" OE2 GLU B  29 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   SER B 101 "
            pdb=" OG1 THR B 105 "
     model   vdw
     2.318 3.040
  ... (remaining 35562 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 7 through 271)
  selection = (chain 'B' and resid 7 through 271)
}

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=0.28 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.300
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.470
  Find NCS groups from input model:        0.060
  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:6.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
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   3671  Z= 0.126
  Angle     :  0.526   5.058   5022  Z= 0.280
  Chirality :  0.034   0.122    634
  Planarity :  0.003   0.027    606
  Dihedral  : 14.272  62.411   1214
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.11 %
    Favored  : 78.21 %
  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:  3.48 (0.40), residues: 466
  helix:  2.94 (0.25), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.00 (0.81), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  44 
 TYR   0.008   0.001   TYR B 206 
 PHE   0.009   0.002   PHE A  93 
 TRP   0.007   0.001   TRP A 199 
 HIS   0.006   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 3670)
  covalent geometry    : angle       0.52631 /  0.28 ( 5020)
  SS BOND              : bond        0.00131 /  0.07 (    1)
  SS BOND              : angle       0.07131 /  0.04 (    2)
  hydrogen bonds       : bond        0.09847 /  6.84 (  280)
  hydrogen bonds       : angle       4.68874 /  3.84 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7605 (mm)
REVERT: B   11 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7608 (mm)
  outliers start: 6
  outliers final: 2
  residues processed: 36
  average time/residue: 0.2459
  time to fit residues: 9.5377
Evaluate side-chains
  32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0170
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5018

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.187504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.143114 restraints weight = 3505.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.77
r_work: 0.3617 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.3487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.0652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3671  Z= 0.147
  Angle     :  0.541   4.949   5022  Z= 0.272
  Chirality :  0.035   0.139    634
  Planarity :  0.004   0.029    606
  Dihedral  :  4.586  28.593    524
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  7.54 %
    Allowed  : 16.48 %
    Favored  : 75.98 %
  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 (0.39), residues: 466
  helix:  2.98 (0.25), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.75 (0.79), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.011   0.001   TYR A 220 
 PHE   0.012   0.002   PHE B  93 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.004   0.001   HIS A 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 3670)
  covalent geometry    : angle       0.54120 /  0.27 ( 5020)
  SS BOND              : bond        0.00077 /  0.04 (    1)
  SS BOND              : angle       0.34404 /  0.19 (    2)
  hydrogen bonds       : bond        0.03464 /  2.48 (  280)
  hydrogen bonds       : angle       3.81467 /  3.00 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 35
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7669 (mm)
REVERT: A   43 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6679 (mp)
REVERT: A  112 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7348 (p)
REVERT: B   11 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7683 (mm)
REVERT: B   43 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6683 (mp)
REVERT: B  112 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7339 (p)
  outliers start: 27
  outliers final: 4
  residues processed: 54
  average time/residue: 0.2541
  time to fit residues: 14.6952
Evaluate side-chains
  41 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  268 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 17 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.4980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.190991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.146437 restraints weight = 3431.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.79
r_work: 0.3629 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (13 function evaluations)
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3671  Z= 0.140
  Angle     :  0.522   5.278   5022  Z= 0.263
  Chirality :  0.036   0.128    634
  Planarity :  0.004   0.028    606
  Dihedral  :  4.337  30.684    520
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.16 %
    Favored  : 78.21 %
  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:  3.53 (0.39), residues: 466
  helix:  2.97 (0.25), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.92 (0.79), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.010   0.002   TYR B 220 
 PHE   0.011   0.002   PHE A  93 
 TRP   0.008   0.001   TRP B 199 
 HIS   0.003   0.001   HIS B 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 3670)
  covalent geometry    : angle       0.52173 /  0.26 ( 5020)
  SS BOND              : bond        0.00064 /  0.03 (    1)
  SS BOND              : angle       0.23637 /  0.13 (    2)
  hydrogen bonds       : bond        0.03243 /  2.30 (  280)
  hydrogen bonds       : angle       3.59857 /  2.78 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7657 (mm)
REVERT: B   11 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7758 (mm)
  outliers start: 13
  outliers final: 5
  residues processed: 41
  average time/residue: 0.2931
  time to fit residues: 12.7378
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  268 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.190132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.145329 restraints weight = 3436.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 1.78
r_work: 0.3605 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3470
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3470 r_free = 0.3470    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3470 r_free = 0.3470    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.3470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3671  Z= 0.147
  Angle     :  0.527   5.461   5022  Z= 0.265
  Chirality :  0.036   0.129    634
  Planarity :  0.004   0.028    606
  Dihedral  :  4.387  31.093    520
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 16.48 %
    Favored  : 78.49 %
  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:  3.48 (0.39), residues: 466
  helix:  2.88 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.76 (0.81), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 257 
 TYR   0.011   0.002   TYR B 220 
 PHE   0.012   0.002   PHE A  93 
 TRP   0.008   0.001   TRP B 199 
 HIS   0.002   0.001   HIS B 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 3670)
  covalent geometry    : angle       0.52699 /  0.27 ( 5020)
  SS BOND              : bond        0.00021 /  0.01 (    1)
  SS BOND              : angle       0.05868 /  0.03 (    2)
  hydrogen bonds       : bond        0.03205 /  2.26 (  280)
  hydrogen bonds       : angle       3.52362 /  2.70 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 29
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7954 (mt)
REVERT: B   11 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7728 (mm)
  outliers start: 18
  outliers final: 8
  residues processed: 43
  average time/residue: 0.2423
  time to fit residues: 11.1410
Evaluate side-chains
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  268 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.187583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142293 restraints weight = 3450.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.77
r_work: 0.3562 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3434
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (13 function evaluations)
r_final: 0.3434
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3671  Z= 0.185
  Angle     :  0.555   5.888   5022  Z= 0.281
  Chirality :  0.037   0.130    634
  Planarity :  0.004   0.028    606
  Dihedral  :  4.680  31.436    520
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.88 %
    Favored  : 77.09 %
  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:  3.23 (0.39), residues: 466
  helix:  2.71 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.81 (0.81), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.011   0.002   TYR B 234 
 PHE   0.015   0.003   PHE B 209 
 TRP   0.011   0.001   TRP A 199 
 HIS   0.003   0.001   HIS B 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.18 ( 3670)
  covalent geometry    : angle       0.55493 /  0.28 ( 5020)
  SS BOND              : bond        0.00157 /  0.08 (    1)
  SS BOND              : angle       0.14859 /  0.08 (    2)
  hydrogen bonds       : bond        0.03437 /  2.41 (  280)
  hydrogen bonds       : angle       3.66225 /  2.80 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 29
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7657 (mm)
REVERT: A   43 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6762 (mp)
REVERT: B   11 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7736 (mm)
REVERT: B   43 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6759 (mp)
  outliers start: 18
  outliers final: 10
  residues processed: 41
  average time/residue: 0.2234
  time to fit residues: 9.9099
Evaluate side-chains
  43 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  268 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.199557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.156266 restraints weight = 3485.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.65
r_work: 0.3685 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3671  Z= 0.155
  Angle     :  0.529   5.687   5022  Z= 0.267
  Chirality :  0.036   0.127    634
  Planarity :  0.004   0.028    606
  Dihedral  :  4.521  31.604    520
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.44 %
    Favored  : 77.65 %
  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 are not related in a simple way.
  whole:  3.27 (0.39), residues: 466
  helix:  2.71 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.74 (0.82), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.011   0.002   TYR B 220 
 PHE   0.012   0.002   PHE B 209 
 TRP   0.008   0.001   TRP B 199 
 HIS   0.002   0.001   HIS B 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 ( 3670)
  covalent geometry    : angle       0.52885 /  0.27 ( 5020)
  SS BOND              : bond        0.00117 /  0.06 (    1)
  SS BOND              : angle       0.13383 /  0.07 (    2)
  hydrogen bonds       : bond        0.03254 /  2.29 (  280)
  hydrogen bonds       : angle       3.55203 /  2.71 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 27
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7750 (mm)
REVERT: B   11 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7798 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 37
  average time/residue: 0.2550
  time to fit residues: 10.1881
Evaluate side-chains
  38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  268 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0000
   overall best weight:    0.4384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.201591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.158707 restraints weight = 3570.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 1.70
r_work: 0.3693 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3671  Z= 0.126
  Angle     :  0.508   5.397   5022  Z= 0.255
  Chirality :  0.035   0.123    634
  Planarity :  0.003   0.028    606
  Dihedral  :  4.318  32.062    520
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 17.32 %
    Favored  : 77.93 %
  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 are not related in a simple way.
  whole:  3.50 (0.39), residues: 466
  helix:  2.88 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.65 (0.82), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  37 
 TYR   0.011   0.002   TYR A 220 
 PHE   0.009   0.002   PHE B 209 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.002   0.001   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 3670)
  covalent geometry    : angle       0.50791 /  0.25 ( 5020)
  SS BOND              : bond        0.00079 /  0.04 (    1)
  SS BOND              : angle       0.12882 /  0.07 (    2)
  hydrogen bonds       : bond        0.03081 /  2.16 (  280)
  hydrogen bonds       : angle       3.43005 /  2.61 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 30
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6701 (mp)
REVERT: B   11 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7807 (mm)
REVERT: B   43 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6705 (mp)
  outliers start: 17
  outliers final: 6
  residues processed: 43
  average time/residue: 0.2066
  time to fit residues: 9.6280
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  112 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0570
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5498

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.199153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.156220 restraints weight = 3508.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 1.62
r_work: 0.3701 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3671  Z= 0.143
  Angle     :  0.528   5.536   5022  Z= 0.264
  Chirality :  0.037   0.167    634
  Planarity :  0.003   0.028    606
  Dihedral  :  4.140  26.698    518
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.27 %
    Favored  : 78.21 %
  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:  3.42 (0.39), residues: 466
  helix:  2.85 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.78 (0.80), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  37 
 TYR   0.012   0.002   TYR A 220 
 PHE   0.012   0.002   PHE B 209 
 TRP   0.008   0.001   TRP B 199 
 HIS   0.002   0.001   HIS B 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 3670)
  covalent geometry    : angle       0.52792 /  0.26 ( 5020)
  SS BOND              : bond        0.00115 /  0.06 (    1)
  SS BOND              : angle       0.14052 /  0.08 (    2)
  hydrogen bonds       : bond        0.03202 /  2.24 (  280)
  hydrogen bonds       : angle       3.43069 /  2.60 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.124 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7783 (mm)
  outliers start: 9
  outliers final: 8
  residues processed: 36
  average time/residue: 0.2479
  time to fit residues: 9.6238
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0020
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.201426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.159034 restraints weight = 3495.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 1.64
r_work: 0.3696 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3559 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3671  Z= 0.134
  Angle     :  0.518   5.501   5022  Z= 0.259
  Chirality :  0.037   0.161    634
  Planarity :  0.004   0.028    606
  Dihedral  :  4.073  26.778    518
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.16 %
    Favored  : 78.21 %
  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:  3.47 (0.40), residues: 466
  helix:  2.88 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.78 (0.81), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.013   0.002   TYR A 220 
 PHE   0.010   0.002   PHE B 209 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.002   0.001   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 3670)
  covalent geometry    : angle       0.51776 /  0.26 ( 5020)
  SS BOND              : bond        0.00124 /  0.07 (    1)
  SS BOND              : angle       0.10376 /  0.06 (    2)
  hydrogen bonds       : bond        0.03124 /  2.19 (  280)
  hydrogen bonds       : angle       3.38701 /  2.56 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 28
  time to evaluate  : 0.120 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7784 (mm)
  outliers start: 13
  outliers final: 8
  residues processed: 39
  average time/residue: 0.2192
  time to fit residues: 9.2755
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.4358

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.202080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.159894 restraints weight = 3556.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 1.66
r_work: 0.3719 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3671  Z= 0.126
  Angle     :  0.513   5.445   5022  Z= 0.256
  Chirality :  0.036   0.160    634
  Planarity :  0.003   0.028    606
  Dihedral  :  4.016  26.970    518
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.27 %
    Favored  : 78.21 %
  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:  3.56 (0.40), residues: 466
  helix:  2.93 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.68 (0.81), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.013   0.002   TYR B 220 
 PHE   0.010   0.002   PHE B 209 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.002   0.001   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 3670)
  covalent geometry    : angle       0.51270 /  0.26 ( 5020)
  SS BOND              : bond        0.00127 /  0.07 (    1)
  SS BOND              : angle       0.13097 /  0.07 (    2)
  hydrogen bonds       : bond        0.03067 /  2.15 (  280)
  hydrogen bonds       : angle       3.36189 /  2.55 (  840)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.135 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 35
  average time/residue: 0.2809
  time to fit residues: 10.5875
Evaluate side-chains
  34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  179 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.4780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.201769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.158958 restraints weight = 3440.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 1.63
r_work: 0.3709 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3671  Z= 0.131
  Angle     :  0.514   5.526   5022  Z= 0.257
  Chirality :  0.036   0.156    634
  Planarity :  0.004   0.028    606
  Dihedral  :  3.829  13.093    516
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.11 %
    Favored  : 78.21 %
  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:  3.52 (0.40), residues: 466
  helix:  2.91 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.72 (0.81), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.014   0.002   TYR A 220 
 PHE   0.011   0.002   PHE B 209 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.002   0.001   HIS B 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 3670)
  covalent geometry    : angle       0.51458 /  0.26 ( 5020)
  SS BOND              : bond        0.00137 /  0.07 (    1)
  SS BOND              : angle       0.08935 /  0.05 (    2)
  hydrogen bonds       : bond        0.03098 /  2.17 (  280)
  hydrogen bonds       : angle       3.37317 /  2.55 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1381.59 seconds
wall clock time: 24 minutes 27.74 seconds (1467.74 seconds total)