Starting phenix.real_space_refine
on Tue Feb  3 12:42:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lja_63140/02_2026/9lja_63140.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lja_63140/02_2026/9lja_63140.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lja_63140/02_2026/9lja_63140.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lja_63140/02_2026/9lja_63140.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lja_63140/02_2026/9lja_63140.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lja_63140/02_2026/9lja_63140.cif"
  }
  resolution = 3.1
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1446      2.51       5
     N     390      2.21       5
     O     471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2313
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 771
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 102, 762
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
      Conformer: "B"
        Number of residues, atoms: 102, 762
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
          bond proxies already assigned to first conformer: 773
  Restraints were copied for chains:
    A, C
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  ALYS B  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  68 " occ=0.50
    residue:
      pdb=" N  ALYS A  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A  68 " occ=0.50
    residue:
      pdb=" N  ALYS C  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS C  68 " occ=0.50
  Time building chain proxies: 0.75, per 1000 atoms: 0.32
  Number of scatterers: 2313
  At special positions: 0
  Unit cell: (74.7, 101.26, 35.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     471      8.00
     N     390      7.00
     C    1446      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  90 " distance=2.02

  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: 0.18
  Conformation dependent library (CDL) restraints added in 170.9 milliseconds
  

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  540

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21
      removed outlier: 6.378A  pdb=" N   SER B  17 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   ILE C  20 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   THR B  19 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   CYS C  22 " --> pdb=" O   THR B  19 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   SER B  21 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 39
      removed outlier: 6.799A  pdb=" N   ASP B  33 " --> pdb=" O   TYR C  34 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   SER C  36 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL B  35 " --> pdb=" O   SER C  36 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   TYR C  38 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TRP B  37 " --> pdb=" O   TYR C  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 53
      removed outlier: 7.147A  pdb=" N   ARG B  47 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   VAL A  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE B  49 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   ASP A  52 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
      removed outlier: 8.858A  pdb=" N   TYR B  51 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU C  53 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 63
      removed outlier: 6.398A  pdb=" N   GLY B  59 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ASP A  62 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   SER B  61 " --> pdb=" O   ASP A  62 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 73
    Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 79
      removed outlier: 8.757A  pdb=" N   ILE B  76 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLY A  79 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   SER B  78 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER C  78 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY B  79 " --> pdb=" O   SER C  78 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101
      removed outlier: 6.400A  pdb=" N   TRP B 100 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)

    26 hydrogen bonds defined for protein.
    75 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.30

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 744
        1.34 -     1.45: 383
        1.45 -     1.56: 1246
        1.56 -     1.67: 0
        1.67 -     1.78: 6
  Bond restraints: 2379
  Sorted by residual:
  bond pdb=" CB  VAL A  50 "
       pdb=" CG1 VAL A  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.74e+00
  bond pdb=" CB  VAL C  50 "
       pdb=" CG1 VAL C  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.69e+00
  bond pdb=" CB  VAL B  50 "
       pdb=" CG1 VAL B  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.66e+00
  bond pdb=" CB  LEU B  53 "
       pdb=" CG  LEU B  53 "
    ideal  model  delta    sigma   weight residual
    1.530  1.508  0.022 2.00e-02 2.50e+03 1.19e+00
  bond pdb=" CB  LEU A  53 "
       pdb=" CG  LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.530  1.508  0.022 2.00e-02 2.50e+03 1.18e+00
  ... (remaining 2374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 3119
        1.91 -     3.82: 97
        3.82 -     5.73: 15
        5.73 -     7.64: 6
        7.64 -     9.54: 3
  Bond angle restraints: 3240
  Sorted by residual:
  angle pdb=" N   GLY A  66 "
        pdb=" CA  GLY A  66 "
        pdb=" C   GLY A  66 "
      ideal   model   delta    sigma   weight residual
     110.42  116.27   -5.85 1.49e+00 4.50e-01 1.54e+01
  angle pdb=" N   GLY B  66 "
        pdb=" CA  GLY B  66 "
        pdb=" C   GLY B  66 "
      ideal   model   delta    sigma   weight residual
     110.42  116.23   -5.81 1.49e+00 4.50e-01 1.52e+01
  angle pdb=" N   GLY C  66 "
        pdb=" CA  GLY C  66 "
        pdb=" C   GLY C  66 "
      ideal   model   delta    sigma   weight residual
     110.42  116.19   -5.77 1.49e+00 4.50e-01 1.50e+01
  angle pdb=" N   PRO B  42 "
        pdb=" CA  PRO B  42 "
        pdb=" C   PRO B  42 "
      ideal   model   delta    sigma   weight residual
     111.22  115.40   -4.18 1.40e+00 5.10e-01 8.90e+00
  angle pdb=" N   PRO A  42 "
        pdb=" CA  PRO A  42 "
        pdb=" C   PRO A  42 "
      ideal   model   delta    sigma   weight residual
     111.22  115.38   -4.16 1.40e+00 5.10e-01 8.85e+00
  ... (remaining 3235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.84: 1120
       11.84 -    23.67: 173
       23.67 -    35.51: 57
       35.51 -    47.34: 9
       47.34 -    59.17: 9
  Dihedral angle restraints: 1368
    sinusoidal: 501
      harmonic: 867
  Sorted by residual:
  dihedral pdb=" CA  GLU A  83 "
           pdb=" C   GLU A  83 "
           pdb=" N   ASP A  84 "
           pdb=" CA  ASP A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.56  -29.44     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  GLU C  83 "
           pdb=" C   GLU C  83 "
           pdb=" N   ASP C  84 "
           pdb=" CA  ASP C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.63  -29.37     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  GLU B  83 "
           pdb=" C   GLU B  83 "
           pdb=" N   ASP B  84 "
           pdb=" CA  ASP B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.67  -29.33     0      5.00e+00 4.00e-02 3.44e+01
  ... (remaining 1365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 152
       0.030 -    0.060: 127
       0.060 -    0.091: 15
       0.091 -    0.121: 37
       0.121 -    0.151: 8
  Chirality restraints: 339
  Sorted by residual:
  chirality pdb=" CA  ILE A  76 "
            pdb=" N   ILE A  76 "
            pdb=" C   ILE A  76 "
            pdb=" CB  ILE A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ILE C  76 "
            pdb=" N   ILE C  76 "
            pdb=" C   ILE C  76 "
            pdb=" CB  ILE C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ILE B  76 "
            pdb=" N   ILE B  76 "
            pdb=" C   ILE B  76 "
            pdb=" CB  ILE B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 336 not shown)

  Planarity restraints: 420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  41 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A  42 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  42 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  42 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  45 "    0.023 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A  46 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  46 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  46 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  45 "    0.023 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO B  46 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "    0.019 5.00e-02 4.00e+02
  ... (remaining 417 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 261
        2.74 -     3.28: 2193
        3.28 -     3.82: 3773
        3.82 -     4.36: 4335
        4.36 -     4.90: 8149
  Nonbonded interactions: 18711
  Sorted by model distance:
  nonbonded pdb=" N   SER B  27 "
            pdb=" O   SER C  27 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" CB  SER B  27 "
            pdb=" O   SER C  27 "
     model   vdw
     2.218 3.440
  nonbonded pdb=" O   SER C  13 "
            pdb=" OG  SER C  13 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER A  13 "
            pdb=" OG  SER A  13 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER B  13 "
            pdb=" OG  SER B  13 "
     model   vdw
     2.260 3.040
  ... (remaining 18706 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.950
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
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      :  0.008   0.044   2382  Z= 0.335
  Angle     :  0.889   9.544   3246  Z= 0.478
  Chirality :  0.052   0.151    339
  Planarity :  0.005   0.034    420
  Dihedral  : 13.353  59.173    819
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.54 (0.28), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.22 (0.21), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  56 
 TYR   0.012   0.002   TYR C  34 
 PHE   0.019   0.003   PHE B 102 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.002   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00751 ( 2379)
  covalent geometry    : angle       0.88822 ( 3240)
  SS BOND              : bond        0.00870 (    3)
  SS BOND              : angle       1.18132 (    6)
  hydrogen bonds       : bond        0.19996 (   26)
  hydrogen bonds       : angle       8.58115 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.089 
Fit side-chains
REVERT: B   11 SER cc_start: 0.8691 (t) cc_final: 0.8484 (p)
REVERT: B   41 HIS cc_start: 0.7398 (m90) cc_final: 0.7150 (m-70)
REVERT: A   47 ARG cc_start: 0.8139 (mtt90) cc_final: 0.6852 (ptt-90)
REVERT: A   56 ARG cc_start: 0.8461 (ptt180) cc_final: 0.5643 (tpm170)
REVERT: A  107 LYS cc_start: 0.6640 (mmtt) cc_final: 0.5292 (pttm)
REVERT: C   23 THR cc_start: 0.8798 (t) cc_final: 0.8579 (p)
REVERT: C   47 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7433 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1296
  time to fit residues: 6.0001
Evaluate side-chains
  27 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
B  71 ASN
A  55 ASN
C  55 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.105139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.091059 restraints weight = 37799.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 4.91
r_work: 0.3025 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2382  Z= 0.183
  Angle     :  0.771   8.419   3246  Z= 0.385
  Chirality :  0.048   0.143    339
  Planarity :  0.004   0.035    420
  Dihedral  :  7.005  26.955    336
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.10 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.05 (0.30), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.23), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 TYR   0.015   0.002   TYR B  51 
 PHE   0.015   0.003   PHE A 102 
 TRP   0.012   0.002   TRP B 100 
 HIS   0.002   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 2379)
  covalent geometry    : angle       0.76925 ( 3240)
  SS BOND              : bond        0.00882 (    3)
  SS BOND              : angle       1.37588 (    6)
  hydrogen bonds       : bond        0.02658 (   26)
  hydrogen bonds       : angle       5.83760 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: B   47 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8411 (mtt180)
REVERT: B   51 TYR cc_start: 0.8459 (t80) cc_final: 0.8235 (t80)
REVERT: A   56 ARG cc_start: 0.8909 (ptt180) cc_final: 0.5894 (tpm170)
REVERT: A  107 LYS cc_start: 0.6943 (mmtt) cc_final: 0.5887 (pttm)
REVERT: C   47 ARG cc_start: 0.8821 (mtt90) cc_final: 0.7740 (mmt-90)
  outliers start: 1
  outliers final: 1
  residues processed: 38
  average time/residue: 0.0954
  time to fit residues: 4.1141
Evaluate side-chains
  31 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.098872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.085571 restraints weight = 36080.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 4.73
r_work: 0.2937 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   2382  Z= 0.315
  Angle     :  0.901   8.874   3246  Z= 0.453
  Chirality :  0.053   0.142    339
  Planarity :  0.005   0.036    420
  Dihedral  :  7.697  24.610    336
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.33 %
    Favored  : 84.67 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.29 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.80 (0.31), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.23), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  56 
 TYR   0.018   0.002   TYR B  51 
 PHE   0.019   0.004   PHE B 102 
 TRP   0.010   0.002   TRP A 100 
 HIS   0.003   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00732 ( 2379)
  covalent geometry    : angle       0.89934 ( 3240)
  SS BOND              : bond        0.01292 (    3)
  SS BOND              : angle       1.58238 (    6)
  hydrogen bonds       : bond        0.03148 (   26)
  hydrogen bonds       : angle       6.04592 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B   23 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8838 (p)
REVERT: A   56 ARG cc_start: 0.8955 (ptt180) cc_final: 0.6004 (tpm170)
REVERT: A  107 LYS cc_start: 0.7585 (mmtt) cc_final: 0.6337 (pttm)
REVERT: C   47 ARG cc_start: 0.8847 (mtt90) cc_final: 0.7585 (mmt-90)
  outliers start: 5
  outliers final: 2
  residues processed: 34
  average time/residue: 0.1133
  time to fit residues: 4.3214
Evaluate side-chains
  32 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain C residue   23 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.106229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.092686 restraints weight = 25083.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 4.33
r_work: 0.3064 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2382  Z= 0.126
  Angle     :  0.708   7.188   3246  Z= 0.350
  Chirality :  0.045   0.147    339
  Planarity :  0.003   0.032    420
  Dihedral  :  6.550  23.460    336
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.49 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.67 (0.31), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.55 (0.24), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  56 
 TYR   0.007   0.001   TYR A  89 
 PHE   0.013   0.002   PHE B 102 
 TRP   0.005   0.001   TRP B 100 
 HIS   0.001   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2379)
  covalent geometry    : angle       0.70647 ( 3240)
  SS BOND              : bond        0.00749 (    3)
  SS BOND              : angle       1.17244 (    6)
  hydrogen bonds       : bond        0.02072 (   26)
  hydrogen bonds       : angle       5.34689 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8903 (ptt180) cc_final: 0.5908 (tpm170)
REVERT: A  107 LYS cc_start: 0.7546 (mmtt) cc_final: 0.6066 (pttm)
REVERT: C   47 ARG cc_start: 0.8802 (mtt90) cc_final: 0.7744 (mmt-90)
  outliers start: 5
  outliers final: 3
  residues processed: 33
  average time/residue: 0.1099
  time to fit residues: 4.0651
Evaluate side-chains
  31 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.100525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.087506 restraints weight = 28307.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 4.37
r_work: 0.2975 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2382  Z= 0.240
  Angle     :  0.811   7.958   3246  Z= 0.404
  Chirality :  0.048   0.142    339
  Planarity :  0.004   0.032    420
  Dihedral  :  7.094  21.953    336
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.00 %
    Favored  : 85.00 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 15.08 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.62 (0.32), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.51 (0.24), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  56 
 TYR   0.008   0.002   TYR C  89 
 PHE   0.017   0.003   PHE B 102 
 TRP   0.007   0.001   TRP A 100 
 HIS   0.002   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 2379)
  covalent geometry    : angle       0.80993 ( 3240)
  SS BOND              : bond        0.00996 (    3)
  SS BOND              : angle       1.30802 (    6)
  hydrogen bonds       : bond        0.02643 (   26)
  hydrogen bonds       : angle       5.48549 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.053 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8940 (ptt180) cc_final: 0.5918 (tpm170)
REVERT: A  107 LYS cc_start: 0.7602 (mmtt) cc_final: 0.6464 (pttm)
REVERT: C   47 ARG cc_start: 0.8851 (mtt90) cc_final: 0.7634 (mmt180)
  outliers start: 3
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1178
  time to fit residues: 3.7653
Evaluate side-chains
  31 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3347 r_free = 0.3347 target = 0.103057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.089794 restraints weight = 29530.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 4.47
r_work: 0.3013 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2382  Z= 0.183
  Angle     :  0.756   7.321   3246  Z= 0.376
  Chirality :  0.046   0.144    339
  Planarity :  0.004   0.034    420
  Dihedral  :  6.834  23.225    336
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 14.29 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.58 (0.32), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.24), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  56 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.015   0.002   PHE A 102 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 2379)
  covalent geometry    : angle       0.75506 ( 3240)
  SS BOND              : bond        0.00927 (    3)
  SS BOND              : angle       1.25986 (    6)
  hydrogen bonds       : bond        0.02312 (   26)
  hydrogen bonds       : angle       5.23869 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8901 (ptt180) cc_final: 0.5898 (tpm170)
REVERT: A  107 LYS cc_start: 0.7682 (mmtt) cc_final: 0.6561 (pttm)
REVERT: C   47 ARG cc_start: 0.8873 (mtt90) cc_final: 0.7654 (mmt-90)
  outliers start: 3
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1281
  time to fit residues: 4.1209
Evaluate side-chains
  30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   overall best weight:    2.0084

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.104716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.091216 restraints weight = 29464.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 4.53
r_work: 0.3034 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2382  Z= 0.142
  Angle     :  0.711   7.092   3246  Z= 0.351
  Chirality :  0.045   0.146    339
  Planarity :  0.003   0.035    420
  Dihedral  :  6.426  20.994    336
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.67 %
    Favored  : 87.33 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.89 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.57 (0.32), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.25), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 TYR   0.006   0.001   TYR B  34 
 PHE   0.014   0.002   PHE B 102 
 TRP   0.005   0.001   TRP B 100 
 HIS   0.002   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 2379)
  covalent geometry    : angle       0.71030 ( 3240)
  SS BOND              : bond        0.00694 (    3)
  SS BOND              : angle       1.02412 (    6)
  hydrogen bonds       : bond        0.01967 (   26)
  hydrogen bonds       : angle       5.02938 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8881 (ptt180) cc_final: 0.5901 (tpm170)
REVERT: A  107 LYS cc_start: 0.7648 (mmtt) cc_final: 0.6613 (pttm)
REVERT: C   47 ARG cc_start: 0.8808 (mtt90) cc_final: 0.7599 (mmt-90)
  outliers start: 3
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1312
  time to fit residues: 4.0845
Evaluate side-chains
  29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0470
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0470
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.4180

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.108521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.094394 restraints weight = 31426.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 4.74
r_work: 0.3080 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2382  Z= 0.115
  Angle     :  0.669   7.067   3246  Z= 0.329
  Chirality :  0.044   0.146    339
  Planarity :  0.003   0.034    420
  Dihedral  :  6.003  20.374    336
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.89 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.50 (0.33), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.25), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.007   0.001   TYR C  51 
 PHE   0.012   0.002   PHE B 102 
 TRP   0.004   0.001   TRP B 100 
 HIS   0.001   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2379)
  covalent geometry    : angle       0.66850 ( 3240)
  SS BOND              : bond        0.00600 (    3)
  SS BOND              : angle       0.98000 (    6)
  hydrogen bonds       : bond        0.01687 (   26)
  hydrogen bonds       : angle       4.83237 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8901 (ptt180) cc_final: 0.5911 (tpm170)
REVERT: A  107 LYS cc_start: 0.7621 (mmtt) cc_final: 0.6594 (pttm)
REVERT: C   47 ARG cc_start: 0.8830 (mtt90) cc_final: 0.7608 (mmt180)
  outliers start: 3
  outliers final: 3
  residues processed: 31
  average time/residue: 0.0735
  time to fit residues: 2.5541
Evaluate side-chains
  31 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 17 optimal weight:    0.3980
   chunk 0 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    0.4980
   chunk 23 optimal weight:    4.9990
   overall best weight:    2.3184

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.104611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.091073 restraints weight = 28107.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 4.45
r_work: 0.3036 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2382  Z= 0.157
  Angle     :  0.719   7.174   3246  Z= 0.355
  Chirality :  0.045   0.144    339
  Planarity :  0.003   0.034    420
  Dihedral  :  6.338  19.399    336
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.00 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 14.29 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.50 (0.33), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.25), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 TYR   0.007   0.001   TYR B  34 
 PHE   0.014   0.002   PHE B 102 
 TRP   0.005   0.001   TRP B 100 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 2379)
  covalent geometry    : angle       0.71830 ( 3240)
  SS BOND              : bond        0.00715 (    3)
  SS BOND              : angle       1.04779 (    6)
  hydrogen bonds       : bond        0.01941 (   26)
  hydrogen bonds       : angle       4.97106 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8908 (ptt180) cc_final: 0.5932 (tpm170)
REVERT: A  107 LYS cc_start: 0.7634 (mmtt) cc_final: 0.6748 (pttm)
REVERT: C   47 ARG cc_start: 0.8818 (mtt90) cc_final: 0.7717 (mmt-90)
  outliers start: 3
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0767
  time to fit residues: 2.4003
Evaluate side-chains
  29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.102425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.089227 restraints weight = 29100.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 4.46
r_work: 0.3004 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2382  Z= 0.194
  Angle     :  0.766   7.518   3246  Z= 0.380
  Chirality :  0.046   0.143    339
  Planarity :  0.004   0.034    420
  Dihedral  :  6.742  22.227    336
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 14.68 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.47 (0.33), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.25), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  56 
 TYR   0.007   0.001   TYR C  34 
 PHE   0.015   0.003   PHE B 102 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 2379)
  covalent geometry    : angle       0.76470 ( 3240)
  SS BOND              : bond        0.00883 (    3)
  SS BOND              : angle       1.18567 (    6)
  hydrogen bonds       : bond        0.02136 (   26)
  hydrogen bonds       : angle       5.12472 (   75)

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

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

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  618 Ramachandran restraints generated.
    309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.052 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.7649 (mmtt) cc_final: 0.6769 (pttm)
REVERT: C   47 ARG cc_start: 0.8834 (mtt90) cc_final: 0.7570 (mmt180)
  outliers start: 3
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0660
  time to fit residues: 2.0927
Evaluate side-chains
  29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   84 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.102739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.089572 restraints weight = 27779.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 4.41
r_work: 0.3008 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2382  Z= 0.183
  Angle     :  0.756   7.242   3246  Z= 0.376
  Chirality :  0.046   0.144    339
  Planarity :  0.004   0.034    420
  Dihedral  :  6.657  21.486    336
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.67 %
    Favored  : 86.33 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 15.08 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.44 (0.33), residues: 309
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.38 (0.25), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  56 
 TYR   0.007   0.001   TYR C  34 
 PHE   0.015   0.002   PHE B 102 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 2379)
  covalent geometry    : angle       0.75506 ( 3240)
  SS BOND              : bond        0.00821 (    3)
  SS BOND              : angle       1.12572 (    6)
  hydrogen bonds       : bond        0.02118 (   26)
  hydrogen bonds       : angle       5.13532 (   75)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 785.83 seconds
wall clock time: 14 minutes 5.01 seconds (845.01 seconds total)