Starting phenix.real_space_refine
on Fri Aug 22 15:23:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b56_44201/08_2025/9b56_44201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b56_44201/08_2025/9b56_44201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b56_44201/08_2025/9b56_44201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b56_44201/08_2025/9b56_44201.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b56_44201/08_2025/9b56_44201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b56_44201/08_2025/9b56_44201.map"
  }
  resolution = 3.35
  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=   0.041
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      14      5.16       5
     C    3110      2.51       5
     N     824      2.21       5
     O     923      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4871
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1162
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 3107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 377, 3099
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 14, 'TRANS': 362}
      Conformer: "B"
        Number of residues, atoms: 377, 3099
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 14, 'TRANS': 362}
          bond proxies already assigned to first conformer: 3161
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.84, per 1000 atoms: 0.38
  Number of scatterers: 4871
  At special positions: 0
  Unit cell: (62.776, 84.056, 104.272, 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      14     16.00
     O     923      8.00
     N     824      7.00
     C    3110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 199.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 6 sheets defined
      48.2% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.736A  pdb=" N   VAL A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
    Processing helix  chain 'A' and resid 130 through 146
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 56 through 60
    Processing helix  chain 'C' and resid 293 through 306
    Processing helix  chain 'C' and resid 307 through 311
      removed outlier: 4.057A  pdb=" N   ALA C 311 " --> pdb=" O   PRO C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 335
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 357 through 374
    Processing helix  chain 'C' and resid 375 through 379
    Processing helix  chain 'C' and resid 395 through 400
      removed outlier: 3.517A  pdb=" N   SER C 398 " --> pdb=" O   PRO C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 420
      removed outlier: 4.313A  pdb=" N   TYR C 406 " --> pdb=" O   ASP C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 437
      removed outlier: 3.651A  pdb=" N   TYR C 433 " --> pdb=" O   VAL C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 444
      No H-bonds generated for 'chain 'C' and resid 442 through 444'
    Processing helix  chain 'C' and resid 445 through 450
      removed outlier: 3.896A  pdb=" N   VAL C 449 " --> pdb=" O   ASP C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 463
    Processing helix  chain 'C' and resid 491 through 495
      removed outlier: 3.725A  pdb=" N   ASN C 494 " --> pdb=" O   ASN C 491 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 501 through 515
    Processing helix  chain 'C' and resid 518 through 533
      removed outlier: 4.236A  pdb=" N   LEU C 532 " --> pdb=" O   GLY C 528 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 539
      removed outlier: 3.680A  pdb=" N   LEU C 538 " --> pdb=" O   PRO C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 544 through 552
    Processing helix  chain 'C' and resid 558 through 564
    Processing helix  chain 'C' and resid 574 through 586
      removed outlier: 3.573A  pdb=" N   PHE C 580 " --> pdb=" O   ILE C 576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 588 through 600
    Processing helix  chain 'C' and resid 638 through 640
      No H-bonds generated for 'chain 'C' and resid 638 through 640'
    Processing helix  chain 'C' and resid 650 through 661
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16
      removed outlier: 9.105A  pdb=" N   LEU B  67 " --> pdb=" O   GLN B   2 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   PHE B   4 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU B  69 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LYS B   6 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321
      removed outlier: 3.654A  pdb=" N   VAL C 321 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 383
    Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 479
      removed outlier: 3.703A  pdb=" N   GLU C 482 " --> pdb=" O   ARG C 479 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568

    216 hydrogen bonds defined for protein.
    605 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: 0.50

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 820
        1.27 -     1.41: 1238
        1.41 -     1.54: 2895
        1.54 -     1.68: 6
        1.68 -     1.82: 24
  Bond restraints: 4983
  Sorted by residual:
  bond pdb=" C04 A1AIV B 101 "
       pdb=" C05 A1AIV B 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.526 -0.073 2.00e-02 2.50e+03 1.33e+01
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  bond pdb=" C05 A1AIV B 101 "
       pdb=" N06 A1AIV B 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 9.43e-01
  bond pdb=" CG  LEU C 595 "
       pdb=" CD2 LEU C 595 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.45e-01
  ... (remaining 4978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.80: 6309
        0.80 -     1.59: 366
        1.59 -     2.39: 32
        2.39 -     3.19: 16
        3.19 -     3.98: 24
  Bond angle restraints: 6747
  Sorted by residual:
  angle pdb=" N   LEU C 424 "
        pdb=" CA  LEU C 424 "
        pdb=" C   LEU C 424 "
      ideal   model   delta    sigma   weight residual
     109.79  107.20    2.59 1.56e+00 4.11e-01 2.75e+00
  angle pdb=" N   ARG A  90 "
        pdb=" CA  ARG A  90 "
        pdb=" C   ARG A  90 "
      ideal   model   delta    sigma   weight residual
     110.80  114.14   -3.34 2.13e+00 2.20e-01 2.46e+00
  angle pdb=" C   PRO A  18 "
        pdb=" N   SER A  19 "
        pdb=" CA  SER A  19 "
      ideal   model   delta    sigma   weight residual
     121.54  124.08   -2.54 1.91e+00 2.74e-01 1.77e+00
  angle pdb=" C03 A1AIV B 101 "
        pdb=" C02 A1AIV B 101 "
        pdb=" N01 A1AIV B 101 "
      ideal   model   delta    sigma   weight residual
     111.06  107.08    3.98 3.00e+00 1.11e-01 1.76e+00
  angle pdb=" N   VAL C 515 "
        pdb=" CA  VAL C 515 "
        pdb=" C   VAL C 515 "
      ideal   model   delta    sigma   weight residual
     109.34  112.10   -2.76 2.08e+00 2.31e-01 1.76e+00
  ... (remaining 6742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.09: 2684
       12.09 -    24.17: 261
       24.17 -    36.26: 55
       36.26 -    48.35: 15
       48.35 -    60.43: 3
  Dihedral angle restraints: 3018
    sinusoidal: 1254
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  LEU A  86 "
           pdb=" C   LEU A  86 "
           pdb=" N   ASP A  87 "
           pdb=" CA  ASP A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.52  -18.48     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  VAL C 515 "
           pdb=" C   VAL C 515 "
           pdb=" N   THR C 516 "
           pdb=" CA  THR C 516 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.46  -16.54     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  TYR C 423 "
           pdb=" C   TYR C 423 "
           pdb=" N   LEU C 424 "
           pdb=" CA  LEU C 424 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.93   15.07     0      5.00e+00 4.00e-02 9.08e+00
  ... (remaining 3015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 450
       0.028 -    0.055: 187
       0.055 -    0.083: 57
       0.083 -    0.110: 27
       0.110 -    0.138: 16
  Chirality restraints: 737
  Sorted by residual:
  chirality pdb=" CA  ILE C 533 "
            pdb=" N   ILE C 533 "
            pdb=" C   ILE C 533 "
            pdb=" CB  ILE C 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ILE A  37 "
            pdb=" N   ILE A  37 "
            pdb=" C   ILE A  37 "
            pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE A  54 "
            pdb=" N   ILE A  54 "
            pdb=" C   ILE A  54 "
            pdb=" CB  ILE A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 734 not shown)

  Planarity restraints: 873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 430 "    0.022 5.00e-02 4.00e+02   3.27e-02 1.71e+00
        pdb=" N   PRO C 431 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 431 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 431 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 646 "   -0.019 5.00e-02 4.00e+02   2.93e-02 1.37e+00
        pdb=" N   PRO C 647 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 647 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 647 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.33e+00
        pdb=" N   PRO A  95 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 870 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.42: 12
        2.42 -     3.04: 3040
        3.04 -     3.66: 6690
        3.66 -     4.28: 10393
        4.28 -     4.90: 17838
  Nonbonded interactions: 37973
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 639 "
            pdb=" C03 A1AIV B 101 "
     model   vdw
     1.794 3.800
  nonbonded pdb=" OE2 GLU A   9 "
            pdb=" OH  TYR A  60 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER C 608 "
            pdb=" OD2 ASP C 612 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" N   CYS A  85 "
            pdb=" O   GLY B  75 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" NH1 ARG C 323 "
            pdb=" OE2 GLU C 364 "
     model   vdw
     2.341 3.120
  ... (remaining 37968 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=0.48 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:             2.420
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     6.340
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   4985  Z= 0.199
  Angle     :  0.463   3.985   6747  Z= 0.232
  Chirality :  0.039   0.138    737
  Planarity :  0.003   0.033    873
  Dihedral  : 10.297  60.433   1878
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  6.63 %
    Favored  : 92.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.36), residues: 594
  helix:  1.52 (0.34), residues: 247
  sheet:  1.38 (0.62), residues: 83
  loop :  0.12 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 479 
 TYR   0.010   0.001   TYR C 419 
 PHE   0.009   0.001   PHE C 407 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.001   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4983)
  covalent geometry    : angle       0.46329 ( 6747)
  hydrogen bonds       : bond        0.14274 (  216)
  hydrogen bonds       : angle       5.57139 (  605)
  Misc. bond           : bond        0.07859 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8069 (mttp)
REVERT: C  613 MET cc_start: 0.8855 (ttt) cc_final: 0.8532 (ttt)
REVERT: C  632 GLN cc_start: 0.8251 (mt0) cc_final: 0.8015 (mt0)
  outliers start: 7
  outliers final: 5
  residues processed: 89
  average time/residue: 0.0683
  time to fit residues: 7.5098
Evaluate side-chains
  59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.145166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.110280 restraints weight = 16223.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 4.80
r_work: 0.3207 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4985  Z= 0.149
  Angle     :  0.536   6.158   6747  Z= 0.277
  Chirality :  0.042   0.124    737
  Planarity :  0.004   0.036    873
  Dihedral  :  5.926  50.427    670
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 11.97 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.36), residues: 594
  helix:  1.53 (0.34), residues: 255
  sheet:  1.31 (0.61), residues: 83
  loop : -0.02 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 143 
 TYR   0.011   0.001   TYR C 419 
 PHE   0.020   0.002   PHE B  45 
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4983)
  covalent geometry    : angle       0.53608 ( 6747)
  hydrogen bonds       : bond        0.04004 (  216)
  hydrogen bonds       : angle       4.54611 (  605)
  Misc. bond           : bond        0.00240 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: B   18 GLU cc_start: 0.8716 (tp30) cc_final: 0.8462 (tp30)
REVERT: C  568 ARG cc_start: 0.8357 (mtt180) cc_final: 0.8069 (mtt90)
REVERT: C  613 MET cc_start: 0.9028 (ttt) cc_final: 0.8723 (ttt)
REVERT: C  632 GLN cc_start: 0.8548 (mt0) cc_final: 0.8333 (mt0)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0592
  time to fit residues: 4.9039
Evaluate side-chains
  53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue  389 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    0.0670
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.145114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.111561 restraints weight = 14926.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 4.62
r_work: 0.3256 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4985  Z= 0.139
  Angle     :  0.514   5.604   6747  Z= 0.266
  Chirality :  0.042   0.187    737
  Planarity :  0.004   0.035    873
  Dihedral  :  5.370  46.027    668
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.97 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.36), residues: 594
  helix:  1.52 (0.34), residues: 255
  sheet:  1.20 (0.60), residues: 85
  loop : -0.07 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 143 
 TYR   0.011   0.001   TYR C 419 
 PHE   0.022   0.002   PHE B  45 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4983)
  covalent geometry    : angle       0.51389 ( 6747)
  hydrogen bonds       : bond        0.03719 (  216)
  hydrogen bonds       : angle       4.45054 (  605)
  Misc. bond           : bond        0.00025 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  568 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8051 (mtt90)
REVERT: C  613 MET cc_start: 0.9043 (ttt) cc_final: 0.8755 (ttt)
REVERT: C  632 GLN cc_start: 0.8484 (mt0) cc_final: 0.8264 (mt0)
  outliers start: 11
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0641
  time to fit residues: 4.7859
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0070
   overall best weight:    0.2754

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.146573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.112673 restraints weight = 16014.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 4.74
r_work: 0.3268 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4985  Z= 0.101
  Angle     :  0.491   7.915   6747  Z= 0.251
  Chirality :  0.041   0.166    737
  Planarity :  0.004   0.037    873
  Dihedral  :  4.950  45.730    666
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.79 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.36), residues: 594
  helix:  1.73 (0.34), residues: 255
  sheet:  1.51 (0.61), residues: 81
  loop : -0.06 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 143 
 TYR   0.012   0.001   TYR A  74 
 PHE   0.019   0.001   PHE B  45 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4983)
  covalent geometry    : angle       0.49136 ( 6747)
  hydrogen bonds       : bond        0.03276 (  216)
  hydrogen bonds       : angle       4.30074 (  605)
  Misc. bond           : bond        0.00042 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: C  568 ARG cc_start: 0.8305 (mtt180) cc_final: 0.8092 (mtt90)
REVERT: C  613 MET cc_start: 0.9030 (ttt) cc_final: 0.8735 (ttt)
REVERT: C  632 GLN cc_start: 0.8505 (mt0) cc_final: 0.8301 (mt0)
  outliers start: 12
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0744
  time to fit residues: 5.8957
Evaluate side-chains
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.145083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.109797 restraints weight = 11608.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 3.49
r_work: 0.3287 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4985  Z= 0.189
  Angle     :  0.565   8.576   6747  Z= 0.285
  Chirality :  0.043   0.171    737
  Planarity :  0.004   0.034    873
  Dihedral  :  5.127  46.055    666
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.34 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.36), residues: 594
  helix:  1.55 (0.34), residues: 254
  sheet:  1.17 (0.59), residues: 85
  loop : -0.22 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 143 
 TYR   0.018   0.001   TYR A  74 
 PHE   0.012   0.002   PHE C 522 
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 4983)
  covalent geometry    : angle       0.56463 ( 6747)
  hydrogen bonds       : bond        0.03916 (  216)
  hydrogen bonds       : angle       4.50118 (  605)
  Misc. bond           : bond        0.00036 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7763 (tp)
REVERT: C  568 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7932 (mtt90)
  outliers start: 14
  outliers final: 10
  residues processed: 60
  average time/residue: 0.0699
  time to fit residues: 5.4103
Evaluate side-chains
  59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain C residue  347 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  466 ASP
Chi-restraints excluded: chain C residue  516 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   chunk 37 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.146125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.112491 restraints weight = 15207.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 4.86
r_work: 0.3226 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4985  Z= 0.142
  Angle     :  0.525   7.726   6747  Z= 0.269
  Chirality :  0.042   0.149    737
  Planarity :  0.004   0.034    873
  Dihedral  :  5.095  46.293    666
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.08 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.36), residues: 594
  helix:  1.59 (0.33), residues: 255
  sheet:  1.14 (0.59), residues: 85
  loop : -0.25 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 143 
 TYR   0.013   0.001   TYR A  74 
 PHE   0.013   0.001   PHE B  45 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4983)
  covalent geometry    : angle       0.52511 ( 6747)
  hydrogen bonds       : bond        0.03606 (  216)
  hydrogen bonds       : angle       4.42001 (  605)
  Misc. bond           : bond        0.00069 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7828 (tp)
REVERT: C  568 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8067 (mtt90)
  outliers start: 11
  outliers final: 10
  residues processed: 59
  average time/residue: 0.0723
  time to fit residues: 5.4874
Evaluate side-chains
  57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain C residue  347 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.0050
   chunk 50 optimal weight:    0.1980
   chunk 42 optimal weight:    0.3980
   chunk 48 optimal weight:    0.3980
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0970
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.1992

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.146504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.112077 restraints weight = 14886.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 4.27
r_work: 0.3280 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4985  Z= 0.097
  Angle     :  0.516   7.675   6747  Z= 0.266
  Chirality :  0.041   0.156    737
  Planarity :  0.004   0.035    873
  Dihedral  :  4.905  45.928    666
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.26 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.36), residues: 594
  helix:  1.78 (0.33), residues: 255
  sheet:  1.50 (0.61), residues: 81
  loop : -0.15 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 143 
 TYR   0.013   0.001   TYR A  74 
 PHE   0.012   0.001   PHE B  45 
 TRP   0.005   0.001   TRP A 141 
 HIS   0.001   0.000   HIS C 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4983)
  covalent geometry    : angle       0.51636 ( 6747)
  hydrogen bonds       : bond        0.03164 (  216)
  hydrogen bonds       : angle       4.27645 (  605)
  Misc. bond           : bond        0.00077 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  568 ARG cc_start: 0.8304 (mtt180) cc_final: 0.8096 (mtt90)
  outliers start: 12
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0657
  time to fit residues: 4.7486
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0070
   chunk 55 optimal weight:    0.0770
   chunk 43 optimal weight:    0.0980
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.148806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.113633 restraints weight = 7496.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.42
r_work: 0.3365 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3376
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4985  Z= 0.105
  Angle     :  0.531   8.502   6747  Z= 0.268
  Chirality :  0.041   0.202    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.799  45.758    666
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 14.00 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.36), residues: 594
  helix:  1.83 (0.33), residues: 255
  sheet:  1.50 (0.61), residues: 81
  loop : -0.14 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 143 
 TYR   0.012   0.001   TYR A  74 
 PHE   0.012   0.001   PHE B  45 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.001   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 4983)
  covalent geometry    : angle       0.53090 ( 6747)
  hydrogen bonds       : bond        0.03163 (  216)
  hydrogen bonds       : angle       4.28663 (  605)
  Misc. bond           : bond        0.00099 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  304 MET cc_start: 0.8573 (ttp) cc_final: 0.7890 (ttt)
  outliers start: 8
  outliers final: 7
  residues processed: 53
  average time/residue: 0.0764
  time to fit residues: 5.3541
Evaluate side-chains
  52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0470
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0170
   chunk 38 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.3516

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.146406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.111701 restraints weight = 11889.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 3.66
r_work: 0.3300 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4985  Z= 0.114
  Angle     :  0.543   9.135   6747  Z= 0.277
  Chirality :  0.041   0.161    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.838  45.764    666
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 14.18 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.36), residues: 594
  helix:  1.83 (0.34), residues: 256
  sheet:  1.39 (0.60), residues: 81
  loop : -0.17 (0.41), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 143 
 TYR   0.012   0.001   TYR A  74 
 PHE   0.021   0.001   PHE B  45 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.003   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4983)
  covalent geometry    : angle       0.54304 ( 6747)
  hydrogen bonds       : bond        0.03315 (  216)
  hydrogen bonds       : angle       4.28904 (  605)
  Misc. bond           : bond        0.00012 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7757 (tp)
REVERT: B   41 GLN cc_start: 0.5731 (pp30) cc_final: 0.5327 (pm20)
REVERT: C  304 MET cc_start: 0.8601 (ttp) cc_final: 0.7906 (ttt)
  outliers start: 8
  outliers final: 7
  residues processed: 53
  average time/residue: 0.0672
  time to fit residues: 4.8281
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  466 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    0.0000
   chunk 12 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0370
   chunk 52 optimal weight:    0.0170
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0060
   overall best weight:    0.0274

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.150596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.116291 restraints weight = 12365.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 4.07
r_work: 0.3328 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4985  Z= 0.095
  Angle     :  0.539   8.871   6747  Z= 0.275
  Chirality :  0.040   0.176    737
  Planarity :  0.004   0.035    873
  Dihedral  :  4.756  45.471    666
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.18 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.36), residues: 594
  helix:  1.94 (0.34), residues: 258
  sheet:  1.39 (0.60), residues: 81
  loop : -0.17 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 143 
 TYR   0.011   0.001   TYR A  74 
 PHE   0.017   0.001   PHE B  45 
 TRP   0.005   0.001   TRP C 459 
 HIS   0.002   0.000   HIS C 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 4983)
  covalent geometry    : angle       0.53918 ( 6747)
  hydrogen bonds       : bond        0.02982 (  216)
  hydrogen bonds       : angle       4.19709 (  605)
  Misc. bond           : bond        0.00027 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: C  613 MET cc_start: 0.8971 (ttm) cc_final: 0.8676 (ttt)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.0597
  time to fit residues: 4.5159
Evaluate side-chains
  56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain C residue  389 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0980
   chunk 54 optimal weight:    0.0270
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4038

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.147915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.113869 restraints weight = 10302.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 3.43
r_work: 0.3347 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4985  Z= 0.123
  Angle     :  0.561   9.511   6747  Z= 0.282
  Chirality :  0.042   0.178    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.808  45.425    666
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.73 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.36), residues: 594
  helix:  1.84 (0.33), residues: 259
  sheet:  1.34 (0.59), residues: 81
  loop : -0.26 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 143 
 TYR   0.011   0.001   TYR A  74 
 PHE   0.015   0.001   PHE B  45 
 TRP   0.009   0.001   TRP C 581 
 HIS   0.002   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4983)
  covalent geometry    : angle       0.56106 ( 6747)
  hydrogen bonds       : bond        0.03239 (  216)
  hydrogen bonds       : angle       4.27456 (  605)
  Misc. bond           : bond        0.00026 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 1142.00 seconds
wall clock time: 19 minutes 59.84 seconds (1199.84 seconds total)