Starting phenix.real_space_refine
on Tue Mar  3 11:42:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wr9_32719/03_2026/7wr9_32719.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wr9_32719/03_2026/7wr9_32719.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wr9_32719/03_2026/7wr9_32719.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wr9_32719/03_2026/7wr9_32719.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wr9_32719/03_2026/7wr9_32719.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wr9_32719/03_2026/7wr9_32719.cif"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.032
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      15      5.16       5
     C    2074      2.51       5
     N     539      2.21       5
     O     638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3266
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 973
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 6, 'TRANS': 120}
    Chain: "B"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 780
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 9, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 1450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1450
          Classifications: {'peptide': 180}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167}
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.90, per 1000 atoms: 0.28
  Number of scatterers: 3266
  At special positions: 0
  Unit cell: (90.48, 63.44, 74.88, 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      15     16.00
     O     638      8.00
     N     539      7.00
     C    2074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 323 " - pdb=" SG  CYS F 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 366 " - pdb=" SG  CYS F 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 467 " - pdb=" SG  CYS F 474 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG C   1 " - " ASN F 330 "
      " NAG F 601 " - " ASN F 357 "
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 194.3 milliseconds
  

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  748

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 8 sheets defined
      3.9% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 4.057A  pdb=" N   THR A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 393 through 397
    Processing helix  chain 'F' and resid 425 through 430
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.997A  pdb=" N   GLN A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 3.518A  pdb=" N   ALA A  92 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ILE A  34 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   LYS A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   THR A  59 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10
      removed outlier: 3.541A  pdb=" N   VAL B  10 " --> pdb=" O   LYS B 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 47
      removed outlier: 6.485A  pdb=" N   TRP B  34 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 341 through 345
      removed outlier: 4.027A  pdb=" N   GLU F 341 " --> pdb=" O   SER F 386 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ASN F 381 " --> pdb=" O   GLU F 502 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 439 through 441

    82 hydrogen bonds defined for protein.
    207 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: 0.45

  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:
        1.20 -     1.32: 525
        1.32 -     1.45: 1011
        1.45 -     1.57: 1802
        1.57 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 3357
  Sorted by residual:
  bond pdb=" C   PRO A 102 "
       pdb=" O   PRO A 102 "
    ideal  model  delta    sigma   weight residual
    1.235  1.196  0.039 1.30e-02 5.92e+03 9.14e+00
  bond pdb=" CA  TYR A 107 "
       pdb=" C   TYR A 107 "
    ideal  model  delta    sigma   weight residual
    1.529  1.498  0.031 1.04e-02 9.25e+03 9.05e+00
  bond pdb=" N   PRO A 102 "
       pdb=" CA  PRO A 102 "
    ideal  model  delta    sigma   weight residual
    1.469  1.432  0.036 1.28e-02 6.10e+03 8.02e+00
  bond pdb=" N   SER A 104 "
       pdb=" CA  SER A 104 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.46e+00
  bond pdb=" N   ASP A 105 "
       pdb=" CA  ASP A 105 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.41e-02 5.03e+03 6.45e+00
  ... (remaining 3352 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 4507
        3.66 -     7.31: 64
        7.31 -    10.97: 6
       10.97 -    14.62: 1
       14.62 -    18.28: 1
  Bond angle restraints: 4579
  Sorted by residual:
  angle pdb=" N   PRO A 106 "
        pdb=" CA  PRO A 106 "
        pdb=" CB  PRO A 106 "
      ideal   model   delta    sigma   weight residual
     103.25   92.17   11.08 1.05e+00 9.07e-01 1.11e+02
  angle pdb=" C   PRO A 106 "
        pdb=" CA  PRO A 106 "
        pdb=" CB  PRO A 106 "
      ideal   model   delta    sigma   weight residual
     111.56  120.78   -9.22 1.65e+00 3.67e-01 3.12e+01
  angle pdb=" CA  LEU B  27 "
        pdb=" CB  LEU B  27 "
        pdb=" CG  LEU B  27 "
      ideal   model   delta    sigma   weight residual
     116.30  134.58  -18.28 3.50e+00 8.16e-02 2.73e+01
  angle pdb=" C   ASP B  91 "
        pdb=" N   ALA B  92 "
        pdb=" CA  ALA B  92 "
      ideal   model   delta    sigma   weight residual
     121.54  130.69   -9.15 1.91e+00 2.74e-01 2.30e+01
  angle pdb=" C   TYR A 107 "
        pdb=" CA  TYR A 107 "
        pdb=" CB  TYR A 107 "
      ideal   model   delta    sigma   weight residual
     111.43  105.49    5.94 1.24e+00 6.50e-01 2.29e+01
  ... (remaining 4574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.95: 1912
       24.95 -    49.89: 95
       49.89 -    74.83: 11
       74.83 -    99.78: 10
       99.78 -   124.72: 5
  Dihedral angle restraints: 2033
    sinusoidal: 847
      harmonic: 1186
  Sorted by residual:
  dihedral pdb=" CA  LEU B  27 "
           pdb=" C   LEU B  27 "
           pdb=" N   PRO B  28 "
           pdb=" CA  PRO B  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.93   34.07     0      5.00e+00 4.00e-02 4.64e+01
  dihedral pdb=" CB  CYS F 467 "
           pdb=" SG  CYS F 467 "
           pdb=" SG  CYS F 474 "
           pdb=" CB  CYS F 474 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.82   44.82     1      1.00e+01 1.00e-02 2.79e+01
  dihedral pdb=" CA  ALA B  92 "
           pdb=" C   ALA B  92 "
           pdb=" N   SER B  93 "
           pdb=" CA  SER B  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.30   25.70     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 2030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 398
       0.061 -    0.121: 86
       0.121 -    0.181: 14
       0.181 -    0.242: 4
       0.242 -    0.302: 3
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" CA  ARG A 100 "
            pdb=" N   ARG A 100 "
            pdb=" C   ARG A 100 "
            pdb=" CB  ARG A 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  TYR A 107 "
            pdb=" N   TYR A 107 "
            pdb=" C   TYR A 107 "
            pdb=" CB  TYR A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 502 not shown)

  Planarity restraints: 587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 109 "    0.017 2.00e-02 2.50e+03   2.81e-02 1.97e+01
        pdb=" CG  TRP A 109 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 109 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 109 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 109 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 109 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 109 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 109 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 109 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 109 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 105 "    0.018 2.00e-02 2.50e+03   3.61e-02 1.31e+01
        pdb=" C   ASP A 105 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   ASP A 105 "    0.023 2.00e-02 2.50e+03
        pdb=" N   PRO A 106 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 118 "    0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   VAL A 118 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   VAL A 118 "    0.023 2.00e-02 2.50e+03
        pdb=" N   TRP A 119 "    0.020 2.00e-02 2.50e+03
  ... (remaining 584 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1152
        2.86 -     3.37: 2584
        3.37 -     3.88: 5412
        3.88 -     4.39: 6083
        4.39 -     4.90: 10951
  Nonbonded interactions: 26182
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 108 "
            pdb=" OG  SER A 111 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   ALA F 430 "
            pdb=" OG1 THR F 485 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG  SER B  93 "
            pdb=" OG1 THR B  95 "
     model   vdw
     2.408 3.040
  nonbonded pdb=" O   GLY B  76 "
            pdb=" NE2 GLN B  78 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" O   SER B  62 "
            pdb=" OG  SER B  62 "
     model   vdw
     2.421 3.040
  ... (remaining 26177 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.510
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.690
  Find NCS groups from input model:        0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
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      :  0.006   0.043   3367  Z= 0.282
  Angle     :  1.055  18.280   4604  Z= 0.592
  Chirality :  0.058   0.302    505
  Planarity :  0.009   0.075    585
  Dihedral  : 17.104 124.722   1270
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  9.63 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  0.86 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -2.72 (0.39), residues: 405
  helix: -4.46 (0.69), residues: 25
  sheet: -1.38 (0.43), residues: 131
  loop : -1.78 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 100 
 TYR   0.040   0.002   TYR F 442 
 PHE   0.030   0.003   PHE F 364 
 TRP   0.072   0.004   TRP A 109 
 HIS   0.002   0.001   HIS B  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 3357)
  covalent geometry    : angle       1.05147 ( 4579)
  SS BOND              : bond        0.00362 (    5)
  SS BOND              : angle       1.29758 (   10)
  hydrogen bonds       : bond        0.26428 (   82)
  hydrogen bonds       : angle       9.68833 (  207)
  link_BETA1-4         : bond        0.00863 (    2)
  link_BETA1-4         : angle       1.85134 (    6)
  link_BETA1-6         : bond        0.00513 (    1)
  link_BETA1-6         : angle       1.12471 (    3)
  link_NAG-ASN         : bond        0.00121 (    2)
  link_NAG-ASN         : angle       1.65290 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 GLU cc_start: 0.6819 (pm20) cc_final: 0.6527 (pt0)
  outliers start: 4
  outliers final: 1
  residues processed: 66
  average time/residue: 0.0795
  time to fit residues: 6.2954
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0570
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.148315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122710 restraints weight = 3924.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.21
r_work: 0.3202 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3367  Z= 0.168
  Angle     :  0.687   9.206   4604  Z= 0.348
  Chirality :  0.046   0.167    505
  Planarity :  0.008   0.118    585
  Dihedral  : 13.396 111.035    561
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.14 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.20 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.39 (0.41), residues: 405
  helix: -4.72 (0.54), residues: 26
  sheet: -1.18 (0.46), residues: 123
  loop : -1.46 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  53 
 TYR   0.014   0.001   TYR F 356 
 PHE   0.014   0.001   PHE F 334 
 TRP   0.028   0.002   TRP A 109 
 HIS   0.004   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3357)
  covalent geometry    : angle       0.68021 ( 4579)
  SS BOND              : bond        0.00275 (    5)
  SS BOND              : angle       1.00553 (   10)
  hydrogen bonds       : bond        0.04594 (   82)
  hydrogen bonds       : angle       7.02129 (  207)
  link_BETA1-4         : bond        0.00899 (    2)
  link_BETA1-4         : angle       2.17646 (    6)
  link_BETA1-6         : bond        0.00687 (    1)
  link_BETA1-6         : angle       1.79445 (    3)
  link_NAG-ASN         : bond        0.00145 (    2)
  link_NAG-ASN         : angle       1.20354 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6969 (p0)
REVERT: B   78 GLN cc_start: 0.7490 (mp10) cc_final: 0.7119 (mp10)
  outliers start: 4
  outliers final: 2
  residues processed: 65
  average time/residue: 0.0797
  time to fit residues: 6.1719
Evaluate side-chains
  62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain B residue   44 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0470
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0870
   chunk 23 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4056

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.151722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.126083 restraints weight = 3901.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.24
r_work: 0.3221 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   3367  Z= 0.128
  Angle     :  0.611   7.522   4604  Z= 0.305
  Chirality :  0.045   0.140    505
  Planarity :  0.007   0.114    585
  Dihedral  : 10.328 101.950    558
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.90 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.34 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.17 (0.42), residues: 405
  helix: -4.59 (0.60), residues: 27
  sheet: -0.99 (0.44), residues: 133
  loop : -1.31 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  53 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.011   0.001   PHE A 101 
 TRP   0.026   0.002   TRP A 109 
 HIS   0.002   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3357)
  covalent geometry    : angle       0.60537 ( 4579)
  SS BOND              : bond        0.00395 (    5)
  SS BOND              : angle       0.62275 (   10)
  hydrogen bonds       : bond        0.03358 (   82)
  hydrogen bonds       : angle       6.22814 (  207)
  link_BETA1-4         : bond        0.00573 (    2)
  link_BETA1-4         : angle       1.81512 (    6)
  link_BETA1-6         : bond        0.00941 (    1)
  link_BETA1-6         : angle       1.83071 (    3)
  link_NAG-ASN         : bond        0.00247 (    2)
  link_NAG-ASN         : angle       0.89697 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.8724 (mt) cc_final: 0.8444 (tp)
REVERT: B   41 GLN cc_start: 0.7381 (pm20) cc_final: 0.7120 (pm20)
REVERT: B   81 ASP cc_start: 0.7685 (m-30) cc_final: 0.7334 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 69
  average time/residue: 0.0868
  time to fit residues: 7.1325
Evaluate side-chains
  66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.0070
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0000
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7004

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.147626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.122023 restraints weight = 3932.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.23
r_work: 0.3190 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   3367  Z= 0.160
  Angle     :  0.617   7.432   4604  Z= 0.310
  Chirality :  0.045   0.145    505
  Planarity :  0.007   0.112    585
  Dihedral  :  9.843 102.120    558
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.64 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.93 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.10 (0.43), residues: 405
  helix: -4.71 (0.49), residues: 27
  sheet: -0.98 (0.44), residues: 133
  loop : -1.21 (0.43), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  60 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.012   0.001   PHE F 334 
 TRP   0.026   0.002   TRP A 109 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 3357)
  covalent geometry    : angle       0.60806 ( 4579)
  SS BOND              : bond        0.00384 (    5)
  SS BOND              : angle       1.44665 (   10)
  hydrogen bonds       : bond        0.03221 (   82)
  hydrogen bonds       : angle       6.17068 (  207)
  link_BETA1-4         : bond        0.00594 (    2)
  link_BETA1-4         : angle       1.85137 (    6)
  link_BETA1-6         : bond        0.00892 (    1)
  link_BETA1-6         : angle       1.85493 (    3)
  link_NAG-ASN         : bond        0.00075 (    2)
  link_NAG-ASN         : angle       1.12498 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8511 (mtm180)
REVERT: A   64 LEU cc_start: 0.8618 (mt) cc_final: 0.8402 (tp)
REVERT: B   41 GLN cc_start: 0.7428 (pm20) cc_final: 0.7174 (pm20)
  outliers start: 9
  outliers final: 7
  residues processed: 68
  average time/residue: 0.0846
  time to fit residues: 6.8006
Evaluate side-chains
  70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0470
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.149311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123313 restraints weight = 3880.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.24
r_work: 0.3186 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   3367  Z= 0.151
  Angle     :  0.630  11.467   4604  Z= 0.310
  Chirality :  0.044   0.149    505
  Planarity :  0.007   0.111    585
  Dihedral  :  9.575 101.247    558
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.64 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.37 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.03 (0.43), residues: 405
  helix: -4.82 (0.38), residues: 27
  sheet: -0.92 (0.44), residues: 133
  loop : -1.15 (0.44), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  53 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.010   0.001   PHE A 101 
 TRP   0.024   0.002   TRP A 109 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3357)
  covalent geometry    : angle       0.62324 ( 4579)
  SS BOND              : bond        0.00438 (    5)
  SS BOND              : angle       1.37876 (   10)
  hydrogen bonds       : bond        0.03096 (   82)
  hydrogen bonds       : angle       5.98196 (  207)
  link_BETA1-4         : bond        0.00536 (    2)
  link_BETA1-4         : angle       1.57693 (    6)
  link_BETA1-6         : bond        0.00918 (    1)
  link_BETA1-6         : angle       1.84748 (    3)
  link_NAG-ASN         : bond        0.00090 (    2)
  link_NAG-ASN         : angle       1.01701 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.8840 (mt) cc_final: 0.8595 (tp)
REVERT: B   78 GLN cc_start: 0.7127 (mp-120) cc_final: 0.6926 (mt0)
  outliers start: 12
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0889
  time to fit residues: 7.0649
Evaluate side-chains
  69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0670
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   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 = 0.3644 r_free = 0.3644 target = 0.146919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.120999 restraints weight = 3933.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.24
r_work: 0.3194 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   3367  Z= 0.155
  Angle     :  0.621   9.733   4604  Z= 0.307
  Chirality :  0.044   0.153    505
  Planarity :  0.007   0.110    585
  Dihedral  :  9.552 100.519    558
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.64 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 15.80 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.96 (0.44), residues: 405
  helix: -4.87 (0.33), residues: 27
  sheet: -0.85 (0.44), residues: 133
  loop : -1.11 (0.44), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  53 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.009   0.001   PHE F 334 
 TRP   0.024   0.002   TRP A 109 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3357)
  covalent geometry    : angle       0.61515 ( 4579)
  SS BOND              : bond        0.00409 (    5)
  SS BOND              : angle       1.20979 (   10)
  hydrogen bonds       : bond        0.03010 (   82)
  hydrogen bonds       : angle       5.94203 (  207)
  link_BETA1-4         : bond        0.00523 (    2)
  link_BETA1-4         : angle       1.49504 (    6)
  link_BETA1-6         : bond        0.00948 (    1)
  link_BETA1-6         : angle       1.87113 (    3)
  link_NAG-ASN         : bond        0.00109 (    2)
  link_NAG-ASN         : angle       0.99757 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8506 (mtm180)
REVERT: B   78 GLN cc_start: 0.7245 (mp-120) cc_final: 0.7038 (mp10)
  outliers start: 14
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0681
  time to fit residues: 5.3748
Evaluate side-chains
  70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Chi-restraints excluded: chain F residue  447 LYS
Chi-restraints excluded: chain F residue  467 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0050
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.149462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.123360 restraints weight = 3977.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.28
r_work: 0.3184 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   3367  Z= 0.138
  Angle     :  0.608   8.665   4604  Z= 0.302
  Chirality :  0.044   0.153    505
  Planarity :  0.007   0.109    585
  Dihedral  :  9.385  98.810    558
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.90 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.38 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.91 (0.44), residues: 405
  helix: -4.91 (0.31), residues: 27
  sheet: -0.80 (0.45), residues: 133
  loop : -1.07 (0.44), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.009   0.001   PHE A 101 
 TRP   0.023   0.002   TRP A 109 
 HIS   0.002   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3357)
  covalent geometry    : angle       0.60206 ( 4579)
  SS BOND              : bond        0.00369 (    5)
  SS BOND              : angle       1.13728 (   10)
  hydrogen bonds       : bond        0.02940 (   82)
  hydrogen bonds       : angle       5.83342 (  207)
  link_BETA1-4         : bond        0.00539 (    2)
  link_BETA1-4         : angle       1.43739 (    6)
  link_BETA1-6         : bond        0.01003 (    1)
  link_BETA1-6         : angle       1.94568 (    3)
  link_NAG-ASN         : bond        0.00113 (    2)
  link_NAG-ASN         : angle       0.86475 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8750 (mtm180) cc_final: 0.8508 (mtm180)
  outliers start: 12
  outliers final: 11
  residues processed: 66
  average time/residue: 0.0703
  time to fit residues: 5.6614
Evaluate side-chains
  70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Chi-restraints excluded: chain F residue  467 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.149682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.124522 restraints weight = 3943.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.19
r_work: 0.3210 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   3367  Z= 0.123
  Angle     :  0.593   7.978   4604  Z= 0.294
  Chirality :  0.044   0.153    505
  Planarity :  0.006   0.108    585
  Dihedral  :  9.107  96.263    558
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.65 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.24 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.85 (0.44), residues: 405
  helix: -4.88 (0.32), residues: 27
  sheet: -0.75 (0.45), residues: 133
  loop : -1.03 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  67 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.009   0.001   PHE A 101 
 TRP   0.022   0.002   TRP A 109 
 HIS   0.002   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3357)
  covalent geometry    : angle       0.58750 ( 4579)
  SS BOND              : bond        0.00322 (    5)
  SS BOND              : angle       1.01359 (   10)
  hydrogen bonds       : bond        0.02808 (   82)
  hydrogen bonds       : angle       5.71648 (  207)
  link_BETA1-4         : bond        0.00529 (    2)
  link_BETA1-4         : angle       1.36303 (    6)
  link_BETA1-6         : bond        0.01087 (    1)
  link_BETA1-6         : angle       2.05685 (    3)
  link_NAG-ASN         : bond        0.00118 (    2)
  link_NAG-ASN         : angle       0.75778 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8678 (mtm180) cc_final: 0.8405 (mtm180)
  outliers start: 11
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0725
  time to fit residues: 5.6452
Evaluate side-chains
  69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Chi-restraints excluded: chain F residue  467 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0870
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.150104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.124896 restraints weight = 3915.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.18
r_work: 0.3210 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   3367  Z= 0.127
  Angle     :  0.589   7.713   4604  Z= 0.292
  Chirality :  0.044   0.155    505
  Planarity :  0.006   0.108    585
  Dihedral  :  8.971  94.837    558
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.41 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.53 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.79 (0.44), residues: 405
  helix: -4.91 (0.30), residues: 27
  sheet: -0.69 (0.45), residues: 133
  loop : -0.99 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.009   0.001   PHE A 101 
 TRP   0.023   0.002   TRP A 109 
 HIS   0.002   0.000   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3357)
  covalent geometry    : angle       0.58404 ( 4579)
  SS BOND              : bond        0.00312 (    5)
  SS BOND              : angle       0.94219 (   10)
  hydrogen bonds       : bond        0.02801 (   82)
  hydrogen bonds       : angle       5.66803 (  207)
  link_BETA1-4         : bond        0.00533 (    2)
  link_BETA1-4         : angle       1.35299 (    6)
  link_BETA1-6         : bond        0.01061 (    1)
  link_BETA1-6         : angle       2.11368 (    3)
  link_NAG-ASN         : bond        0.00115 (    2)
  link_NAG-ASN         : angle       0.75540 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8694 (mtm180) cc_final: 0.8061 (mtm180)
REVERT: F  366 CYS cc_start: 0.7422 (m) cc_final: 0.7034 (m)
  outliers start: 11
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0710
  time to fit residues: 5.6329
Evaluate side-chains
  69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Chi-restraints excluded: chain F residue  467 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 34 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.147808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121791 restraints weight = 3907.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.23
r_work: 0.3183 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   3367  Z= 0.155
  Angle     :  0.610   8.043   4604  Z= 0.304
  Chirality :  0.044   0.155    505
  Planarity :  0.006   0.108    585
  Dihedral  :  9.158  96.479    558
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.40 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.53 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.79 (0.44), residues: 405
  helix: -4.93 (0.29), residues: 27
  sheet: -0.71 (0.45), residues: 133
  loop : -0.98 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  53 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.009   0.001   PHE F 334 
 TRP   0.024   0.002   TRP A 109 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3357)
  covalent geometry    : angle       0.60512 ( 4579)
  SS BOND              : bond        0.00370 (    5)
  SS BOND              : angle       0.97193 (   10)
  hydrogen bonds       : bond        0.02901 (   82)
  hydrogen bonds       : angle       5.74932 (  207)
  link_BETA1-4         : bond        0.00522 (    2)
  link_BETA1-4         : angle       1.41395 (    6)
  link_BETA1-6         : bond        0.00998 (    1)
  link_BETA1-6         : angle       2.02883 (    3)
  link_NAG-ASN         : bond        0.00162 (    2)
  link_NAG-ASN         : angle       0.94503 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8721 (mtm180) cc_final: 0.8459 (mtm180)
REVERT: F  366 CYS cc_start: 0.7383 (m) cc_final: 0.6993 (m)
  outliers start: 10
  outliers final: 10
  residues processed: 65
  average time/residue: 0.0705
  time to fit residues: 5.5764
Evaluate side-chains
  69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue  109 TRP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain F residue  385 ASP
Chi-restraints excluded: chain F residue  404 VAL
Chi-restraints excluded: chain F residue  467 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.151462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.125129 restraints weight = 3930.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.27
r_work: 0.3208 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   3367  Z= 0.123
  Angle     :  0.588   7.890   4604  Z= 0.292
  Chirality :  0.044   0.153    505
  Planarity :  0.006   0.107    585
  Dihedral  :  8.905  93.754    558
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.16 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.39 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.74 (0.44), residues: 405
  helix: -4.91 (0.30), residues: 27
  sheet: -0.62 (0.45), residues: 133
  loop : -0.98 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.012   0.001   TYR F 356 
 PHE   0.009   0.001   PHE A 101 
 TRP   0.023   0.002   TRP A 109 
 HIS   0.002   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3357)
  covalent geometry    : angle       0.58309 ( 4579)
  SS BOND              : bond        0.00288 (    5)
  SS BOND              : angle       0.89053 (   10)
  hydrogen bonds       : bond        0.02745 (   82)
  hydrogen bonds       : angle       5.62457 (  207)
  link_BETA1-4         : bond        0.00531 (    2)
  link_BETA1-4         : angle       1.32502 (    6)
  link_BETA1-6         : bond        0.01059 (    1)
  link_BETA1-6         : angle       2.13714 (    3)
  link_NAG-ASN         : bond        0.00109 (    2)
  link_NAG-ASN         : angle       0.70721 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1140.69 seconds
wall clock time: 20 minutes 7.16 seconds (1207.16 seconds total)