Starting phenix.real_space_refine
on Wed Sep 17 04:00:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mek_48216/09_2025/9mek_48216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mek_48216/09_2025/9mek_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_48216/09_2025/9mek_48216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mek_48216/09_2025/9mek_48216.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mek_48216/09_2025/9mek_48216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mek_48216/09_2025/9mek_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3594
  Number of models: 1
  Model: ""
    Number of chains: 3
    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: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 11
          Unusual residues: {'  K': 4, 'HP6': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.27, per 1000 atoms: 0.35
  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: 0.43
  Conformation dependent library (CDL) restraints added in 133.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.06
  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: 0.42

  Time building geometry restraints manager: 0.40 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:             5.040
  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:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.070
  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:6.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
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 aren 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
  covalent geometry    : bond        0.00275 ( 3670)
  covalent geometry    : angle       0.52631 ( 5020)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.07131 (    2)
  hydrogen bonds       : bond        0.09847 (  280)
  hydrogen bonds       : angle       4.68874 (  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  : 0.126 
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: 0.2473
  time to fit residues: 9.5956
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  : 0.124 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4218

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.190684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.145787 restraints weight = 3382.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.76
r_work: 0.3596 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.0594

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= 0.131
  Angle     :  0.516   4.955   5022  Z= 0.258
  Chirality :  0.035   0.137    634
  Planarity :  0.004   0.029    606
  Dihedral  :  4.297  28.937    524
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 16.76 %
    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 aren not related in a simple way.
  whole:  3.66 (0.40), residues: 466
  helix:  3.02 (0.25), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.62 (0.82), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.009   0.001   TYR B 220 
 PHE   0.011   0.002   PHE B  93 
 TRP   0.006   0.001   TRP B 199 
 HIS   0.003   0.001   HIS A 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3670)
  covalent geometry    : angle       0.51613 ( 5020)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.47639 (    2)
  hydrogen bonds       : bond        0.03324 (  280)
  hydrogen bonds       : angle       3.73403 (  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
  58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 32
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7733 (mm)
REVERT: A   43 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6799 (mt)
REVERT: A  112 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7327 (p)
REVERT: B   11 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7760 (mm)
REVERT: B   43 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6779 (mt)
REVERT: B  112 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7330 (p)
  outliers start: 26
  outliers final: 3
  residues processed: 51
  average time/residue: 0.2756
  time to fit residues: 14.9743
Evaluate side-chains
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0040
   chunk 17 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.187078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.141180 restraints weight = 3344.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 1.77
r_work: 0.3595 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.0877

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     :  0.502   5.199   5022  Z= 0.252
  Chirality :  0.035   0.133    634
  Planarity :  0.003   0.028    606
  Dihedral  :  4.097  30.871    520
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.88 %
    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 aren not related in a simple way.
  whole:  3.66 (0.40), residues: 466
  helix:  2.99 (0.25), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.47 (0.86), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.009   0.001   TYR A 206 
 PHE   0.011   0.002   PHE A  93 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.003   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3670)
  covalent geometry    : angle       0.50168 ( 5020)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.20914 (    2)
  hydrogen bonds       : bond        0.03175 (  280)
  hydrogen bonds       : angle       3.52927 (  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
  47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7890 (mt)
REVERT: A   43 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6655 (mp)
REVERT: A  112 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7317 (p)
REVERT: B   11 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7655 (mm)
REVERT: B  112 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7302 (p)
  outliers start: 14
  outliers final: 5
  residues processed: 42
  average time/residue: 0.2995
  time to fit residues: 13.2722
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  : 0.133 
-------------------------------------------------------------------------------
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  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  112 THR
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:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.189169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.143105 restraints weight = 3347.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.80
r_work: 0.3572 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
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 = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3434
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3671  Z= 0.150
  Angle     :  0.514   5.457   5022  Z= 0.260
  Chirality :  0.036   0.138    634
  Planarity :  0.003   0.028    606
  Dihedral  :  4.253  31.120    520
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 16.48 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.54 (0.40), residues: 466
  helix:  2.88 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.45 (0.86), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.010   0.002   TYR A 206 
 PHE   0.012   0.002   PHE B  93 
 TRP   0.008   0.001   TRP A 199 
 HIS   0.002   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3670)
  covalent geometry    : angle       0.51440 ( 5020)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.03362 (    2)
  hydrogen bonds       : bond        0.03245 (  280)
  hydrogen bonds       : angle       3.51951 (  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
  44 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 28
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  112 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7309 (p)
REVERT: B   11 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7636 (mm)
REVERT: B  112 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7285 (p)
  outliers start: 16
  outliers final: 6
  residues processed: 40
  average time/residue: 0.1959
  time to fit residues: 8.5625
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  : 0.146 
-------------------------------------------------------------------------------
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 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:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.191340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145560 restraints weight = 3305.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 1.80
r_work: 0.3593 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3671  Z= 0.112
  Angle     :  0.484   5.150   5022  Z= 0.242
  Chirality :  0.034   0.128    634
  Planarity :  0.003   0.028    606
  Dihedral  :  3.733  25.759    518
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.27 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.76 (0.40), residues: 466
  helix:  3.03 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.36 (0.87), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  35 
 TYR   0.010   0.001   TYR A 206 
 PHE   0.009   0.002   PHE A 122 
 TRP   0.006   0.001   TRP B 199 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3670)
  covalent geometry    : angle       0.48415 ( 5020)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.05298 (    2)
  hydrogen bonds       : bond        0.02963 (  280)
  hydrogen bonds       : angle       3.33049 (  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
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B  112 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7328 (p)
  outliers start: 12
  outliers final: 6
  residues processed: 38
  average time/residue: 0.2363
  time to fit residues: 9.6689
Evaluate side-chains
  34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
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  268 LEU
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  112 THR
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:    0.8980
   chunk 40 optimal weight:    0.0870
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0980
   chunk 22 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.4154 r_free = 0.4154 target = 0.190415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144337 restraints weight = 3315.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 1.81
r_work: 0.3587 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1209

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= 0.121
  Angle     :  0.497   5.215   5022  Z= 0.250
  Chirality :  0.035   0.152    634
  Planarity :  0.003   0.027    606
  Dihedral  :  3.589  13.484    516
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.83 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.72 (0.40), residues: 466
  helix:  3.00 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.40 (0.86), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  37 
 TYR   0.010   0.002   TYR B 206 
 PHE   0.010   0.002   PHE A  93 
 TRP   0.007   0.001   TRP A 199 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3670)
  covalent geometry    : angle       0.49706 ( 5020)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.02879 (    2)
  hydrogen bonds       : bond        0.03006 (  280)
  hydrogen bonds       : angle       3.33025 (  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
  38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 28
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 38
  average time/residue: 0.2491
  time to fit residues: 10.1975
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  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   54 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:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0670
   overall best weight:    0.6718

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.199995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.154447 restraints weight = 3423.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.67
r_work: 0.3653 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3671  Z= 0.159
  Angle     :  0.534   5.719   5022  Z= 0.271
  Chirality :  0.037   0.138    634
  Planarity :  0.004   0.028    606
  Dihedral  :  3.875  16.475    516
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.32 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.53 (0.40), residues: 466
  helix:  2.87 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.46 (0.85), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.010   0.002   TYR A 220 
 PHE   0.013   0.002   PHE B  93 
 TRP   0.009   0.001   TRP A 199 
 HIS   0.002   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3670)
  covalent geometry    : angle       0.53412 ( 5020)
  SS BOND              : bond        0.00147 (    1)
  SS BOND              : angle       0.08206 (    2)
  hydrogen bonds       : bond        0.03241 (  280)
  hydrogen bonds       : angle       3.46171 (  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
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 29
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7819 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 39
  average time/residue: 0.2388
  time to fit residues: 10.1381
Evaluate side-chains
  38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  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  268 LEU
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  179 VAL
Chi-restraints excluded: chain B residue  268 LEU
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:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   chunk 42 optimal weight:    0.0020
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.4276 r_free = 0.4276 target = 0.200924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155569 restraints weight = 3360.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 1.66
r_work: 0.3684 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3671  Z= 0.113
  Angle     :  0.512   5.177   5022  Z= 0.257
  Chirality :  0.035   0.136    634
  Planarity :  0.003   0.028    606
  Dihedral  :  3.587  13.065    516
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.44 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.78 (0.40), residues: 466
  helix:  3.04 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.33 (0.87), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  37 
 TYR   0.010   0.002   TYR A 206 
 PHE   0.009   0.002   PHE B 122 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3670)
  covalent geometry    : angle       0.51257 ( 5020)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.05395 (    2)
  hydrogen bonds       : bond        0.02954 (  280)
  hydrogen bonds       : angle       3.30815 (  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
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7788 (mm)
  outliers start: 10
  outliers final: 5
  residues processed: 40
  average time/residue: 0.2464
  time to fit residues: 10.6561
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  : 0.123 
-------------------------------------------------------------------------------
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 B residue   11 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   76 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0270
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0020
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4246

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.200350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.155476 restraints weight = 3308.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 1.62
r_work: 0.3681 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1371

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= 0.124
  Angle     :  0.527   5.340   5022  Z= 0.262
  Chirality :  0.035   0.131    634
  Planarity :  0.003   0.028    606
  Dihedral  :  3.644  13.551    516
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.72 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.72 (0.40), residues: 466
  helix:  3.01 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.44 (0.85), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  37 
 TYR   0.011   0.002   TYR A 220 
 PHE   0.010   0.002   PHE A 122 
 TRP   0.007   0.001   TRP B 199 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3670)
  covalent geometry    : angle       0.52720 ( 5020)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.07721 (    2)
  hydrogen bonds       : bond        0.02987 (  280)
  hydrogen bonds       : angle       3.26362 (  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
  39 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7772 (mm)
REVERT: B  112 THR cc_start: 0.7811 (m) cc_final: 0.7599 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 39
  average time/residue: 0.2456
  time to fit residues: 10.3673
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  : 0.134 
-------------------------------------------------------------------------------
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 B residue   11 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   76 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:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4250 r_free = 0.4250 target = 0.199186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.155216 restraints weight = 3319.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.83
r_work: 0.3676 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3542 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1443

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= 0.137
  Angle     :  0.538   5.504   5022  Z= 0.270
  Chirality :  0.037   0.166    634
  Planarity :  0.003   0.027    606
  Dihedral  :  3.744  14.881    516
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.39 %
    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 aren not related in a simple way.
  whole:  3.62 (0.40), residues: 466
  helix:  2.95 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.50 (0.85), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.012   0.002   TYR A 220 
 PHE   0.010   0.002   PHE A 122 
 TRP   0.008   0.001   TRP A 199 
 HIS   0.002   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3670)
  covalent geometry    : angle       0.53844 ( 5020)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.08516 (    2)
  hydrogen bonds       : bond        0.03114 (  280)
  hydrogen bonds       : angle       3.33727 (  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
  35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.139 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7870 (mm)
  outliers start: 6
  outliers final: 4
  residues processed: 35
  average time/residue: 0.2757
  time to fit residues: 10.3972
Evaluate side-chains
  34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue   54 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.0010
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4786

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.200034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.157222 restraints weight = 3309.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 1.71
r_work: 0.3672 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1462

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= 0.128
  Angle     :  0.505   5.430   5022  Z= 0.252
  Chirality :  0.036   0.169    634
  Planarity :  0.003   0.028    606
  Dihedral  :  3.695  14.284    516
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 20.11 %
    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 aren not related in a simple way.
  whole:  3.66 (0.40), residues: 466
  helix:  2.96 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.43 (0.85), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.011   0.002   TYR B 220 
 PHE   0.010   0.002   PHE A 122 
 TRP   0.008   0.001   TRP A 199 
 HIS   0.002   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3670)
  covalent geometry    : angle       0.50480 ( 5020)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.07274 (    2)
  hydrogen bonds       : bond        0.03056 (  280)
  hydrogen bonds       : angle       3.32082 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1408.02 seconds
wall clock time: 24 minutes 51.18 seconds (1491.18 seconds total)