Starting phenix.real_space_refine
on Tue Feb  3 16:42:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jxl_61867/02_2026/9jxl_61867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jxl_61867/02_2026/9jxl_61867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jxl_61867/02_2026/9jxl_61867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jxl_61867/02_2026/9jxl_61867.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jxl_61867/02_2026/9jxl_61867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jxl_61867/02_2026/9jxl_61867.cif"
  }
  resolution = 3.23
  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=   0.005 sd=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      21      5.16       5
     C    3296      2.51       5
     N     825      2.21       5
     O     873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5018
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 5003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 604, 5003
          Classifications: {'peptide': 604}
          Link IDs: {'PTRANS': 20, 'TRANS': 583}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 15
          Unusual residues: {'PO4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.30, per 1000 atoms: 0.26
  Number of scatterers: 5018
  At special positions: 0
  Unit cell: (98.115, 71.74, 101.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P       3     15.00
     O     873      8.00
     N     825      7.00
     C    3296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 305.5 milliseconds
  

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      79.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 12 through 19
      removed outlier: 3.555A  pdb=" N   ARG B  16 " --> pdb=" O   PRO B  13 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   LYS B  17 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR B  19 " --> pdb=" O   ARG B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 35
      removed outlier: 3.632A  pdb=" N   PHE B  25 " --> pdb=" O   GLN B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 99
      removed outlier: 3.895A  pdb=" N   LYS B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 168
    Processing helix  chain 'B' and resid 170 through 180
    Processing helix  chain 'B' and resid 181 through 183
      No H-bonds generated for 'chain 'B' and resid 181 through 183'
    Processing helix  chain 'B' and resid 190 through 207
      removed outlier: 3.557A  pdb=" N   GLU B 207 " --> pdb=" O   THR B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 219
    Processing helix  chain 'B' and resid 230 through 259
      removed outlier: 4.171A  pdb=" N   LEU B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 272
    Processing helix  chain 'B' and resid 272 through 296
      removed outlier: 3.640A  pdb=" N   PHE B 276 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
      removed outlier: 3.729A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.539A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 3.638A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 382
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.886A  pdb=" N   ASN B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 420
    Processing helix  chain 'B' and resid 449 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 478
      removed outlier: 4.110A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 502
      removed outlier: 3.968A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 533
      removed outlier: 3.663A  pdb=" N   ASP B 533 " --> pdb=" O   ASP B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 581
      removed outlier: 3.518A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TRP B 573 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE B 575 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   GLN B 576 " --> pdb=" O   ALA B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 622
      removed outlier: 4.325A  pdb=" N   ASP B 590 " --> pdb=" O   PRO B 586 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.787A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN B 618 " --> pdb=" O   ASN B 614 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN B 619 " --> pdb=" O   GLU B 615 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY B 621 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU B 622 " --> pdb=" O   ASN B 618 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    1041 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: 0.46

  Time building geometry restraints manager: 0.60 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: 885
        1.32 -     1.44: 1424
        1.44 -     1.56: 2817
        1.56 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 5156
  Sorted by residual:
  bond pdb=" CA  SER B 264 "
       pdb=" CB  SER B 264 "
    ideal  model  delta    sigma   weight residual
    1.524  1.450  0.074 1.27e-02 6.20e+03 3.43e+01
  bond pdb=" CA  ALA B 449 "
       pdb=" CB  ALA B 449 "
    ideal  model  delta    sigma   weight residual
    1.533  1.480  0.053 1.46e-02 4.69e+03 1.31e+01
  bond pdb=" O3  PO4 B 702 "
       pdb=" P   PO4 B 702 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.84e+00
  bond pdb=" O3  PO4 B 701 "
       pdb=" P   PO4 B 701 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" O3  PO4 B 703 "
       pdb=" P   PO4 B 703 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.71e+00
  ... (remaining 5151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 6838
        2.17 -     4.35: 121
        4.35 -     6.52: 25
        6.52 -     8.69: 4
        8.69 -    10.87: 3
  Bond angle restraints: 6991
  Sorted by residual:
  angle pdb=" CA  PHE B 394 "
        pdb=" CB  PHE B 394 "
        pdb=" CG  PHE B 394 "
      ideal   model   delta    sigma   weight residual
     113.80  121.68   -7.88 1.00e+00 1.00e+00 6.20e+01
  angle pdb=" N   ARG B 448 "
        pdb=" CA  ARG B 448 "
        pdb=" C   ARG B 448 "
      ideal   model   delta    sigma   weight residual
     114.12  104.10   10.02 1.39e+00 5.18e-01 5.20e+01
  angle pdb=" N   GLN B 452 "
        pdb=" CA  GLN B 452 "
        pdb=" C   GLN B 452 "
      ideal   model   delta    sigma   weight residual
     113.88  105.78    8.10 1.23e+00 6.61e-01 4.34e+01
  angle pdb=" C   SER B 264 "
        pdb=" N   ILE B 265 "
        pdb=" CA  ILE B 265 "
      ideal   model   delta    sigma   weight residual
     121.97  111.10   10.87 1.80e+00 3.09e-01 3.64e+01
  angle pdb=" C   ASP B 393 "
        pdb=" CA  ASP B 393 "
        pdb=" CB  ASP B 393 "
      ideal   model   delta    sigma   weight residual
     110.70  119.47   -8.77 1.83e+00 2.99e-01 2.30e+01
  ... (remaining 6986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 2630
       16.69 -    33.38: 279
       33.38 -    50.06: 80
       50.06 -    66.75: 12
       66.75 -    83.44: 2
  Dihedral angle restraints: 3003
    sinusoidal: 1215
      harmonic: 1788
  Sorted by residual:
  dihedral pdb=" CA  ALA B 384 "
           pdb=" C   ALA B 384 "
           pdb=" N   PRO B 385 "
           pdb=" CA  PRO B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.99   30.01     0      5.00e+00 4.00e-02 3.60e+01
  dihedral pdb=" CA  LEU B 477 "
           pdb=" C   LEU B 477 "
           pdb=" N   VAL B 478 "
           pdb=" CA  VAL B 478 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.64   25.36     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  MET B 532 "
           pdb=" C   MET B 532 "
           pdb=" N   ASP B 533 "
           pdb=" CA  ASP B 533 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 3000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 598
       0.051 -    0.102: 135
       0.102 -    0.153: 24
       0.153 -    0.204: 4
       0.204 -    0.256: 1
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CA  VAL B 447 "
            pdb=" N   VAL B 447 "
            pdb=" C   VAL B 447 "
            pdb=" CB  VAL B 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  VAL B 509 "
            pdb=" N   VAL B 509 "
            pdb=" C   VAL B 509 "
            pdb=" CB  VAL B 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" CA  ASP B 393 "
            pdb=" N   ASP B 393 "
            pdb=" C   ASP B 393 "
            pdb=" CB  ASP B 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.76e-01
  ... (remaining 759 not shown)

  Planarity restraints: 869
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 506 "   -0.013 2.00e-02 2.50e+03   2.56e-02 6.53e+00
        pdb=" C   ASP B 506 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASP B 506 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR B 507 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 509 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.04e+00
        pdb=" C   VAL B 509 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL B 509 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   PHE B 510 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 384 "    0.040 5.00e-02 4.00e+02   6.08e-02 5.92e+00
        pdb=" N   PRO B 385 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 385 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 385 "    0.034 5.00e-02 4.00e+02
  ... (remaining 866 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 10
        2.29 -     2.94: 2304
        2.94 -     3.59: 7535
        3.59 -     4.25: 11497
        4.25 -     4.90: 19843
  Nonbonded interactions: 41189
  Sorted by model distance:
  nonbonded pdb=" SD  MET B 408 "
            pdb=" NE2 GLN B 452 "
     model   vdw
     1.633 3.480
  nonbonded pdb=" CE  MET B 408 "
            pdb=" OG1 THR B 580 "
     model   vdw
     2.057 3.460
  nonbonded pdb=" OE1 GLN B  18 "
            pdb=" CD1 PHE B  72 "
     model   vdw
     2.147 3.340
  nonbonded pdb=" O   ALA B 449 "
            pdb=" N   GLN B 452 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OE1 GLN B  18 "
            pdb=" CE1 PHE B  72 "
     model   vdw
     2.211 3.340
  ... (remaining 41184 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.350
  Find NCS groups from input model:        0.020
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
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      :  0.007   0.074   5157  Z= 0.354
  Angle     :  0.759  10.866   6993  Z= 0.486
  Chirality :  0.045   0.256    762
  Planarity :  0.004   0.061    869
  Dihedral  : 14.723  83.438   1840
  Min Nonbonded Distance : 1.633

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 12.34 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.36 (0.31), residues: 598
  helix: -0.01 (0.22), residues: 441
  sheet:  None (None), residues: 0
  loop : -3.38 (0.40), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 627 
 TYR   0.016   0.002   TYR B 148 
 PHE   0.013   0.002   PHE B  54 
 TRP   0.038   0.002   TRP B 395 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00697 ( 5156)
  covalent geometry    : angle       0.75896 ( 6991)
  SS BOND              : bond        0.00413 (    1)
  SS BOND              : angle       0.57688 (    2)
  hydrogen bonds       : bond        0.12814 (  349)
  hydrogen bonds       : angle       5.81569 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B  272 TYR cc_start: 0.8961 (m-80) cc_final: 0.8201 (m-80)
REVERT: B  448 ARG cc_start: 0.7126 (ttm110) cc_final: 0.6902 (mtm-85)
REVERT: B  468 ARG cc_start: 0.8004 (tmt170) cc_final: 0.7073 (mtt180)
  outliers start: 1
  outliers final: 1
  residues processed: 82
  average time/residue: 0.0670
  time to fit residues: 6.8877
Evaluate side-chains
  54 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  394 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0060
   chunk 31 optimal weight:    0.0570
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4314

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
B 399 GLN
B 479 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.139636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.101020 restraints weight = 6863.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.99
r_work: 0.2958 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5157  Z= 0.130
  Angle     :  0.528   5.848   6993  Z= 0.288
  Chirality :  0.039   0.126    762
  Planarity :  0.004   0.053    869
  Dihedral  :  4.710  29.316    663
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.58 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.34), residues: 598
  helix:  1.57 (0.24), residues: 442
  sheet:  None (None), residues: 0
  loop : -3.00 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 448 
 TYR   0.013   0.001   TYR B 496 
 PHE   0.021   0.001   PHE B 394 
 TRP   0.015   0.001   TRP B 395 
 HIS   0.003   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5156)
  covalent geometry    : angle       0.52776 ( 6991)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.65524 (    2)
  hydrogen bonds       : bond        0.04302 (  349)
  hydrogen bonds       : angle       3.97249 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.116 
Fit side-chains
REVERT: B  272 TYR cc_start: 0.9111 (m-80) cc_final: 0.8342 (m-80)
REVERT: B  426 SER cc_start: 0.8890 (m) cc_final: 0.8678 (p)
REVERT: B  468 ARG cc_start: 0.8277 (tmt170) cc_final: 0.6504 (mtt180)
REVERT: B  511 PHE cc_start: 0.9028 (t80) cc_final: 0.8800 (t80)
  outliers start: 8
  outliers final: 1
  residues processed: 67
  average time/residue: 0.0698
  time to fit residues: 5.9633
Evaluate side-chains
  53 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.136477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.097375 restraints weight = 6865.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.99
r_work: 0.2903 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5157  Z= 0.149
  Angle     :  0.518   6.207   6993  Z= 0.276
  Chirality :  0.039   0.137    762
  Planarity :  0.004   0.056    869
  Dihedral  :  4.523  28.762    661
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.01 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.35), residues: 598
  helix:  2.07 (0.24), residues: 442
  sheet:  None (None), residues: 0
  loop : -2.61 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 472 
 TYR   0.016   0.001   TYR B 352 
 PHE   0.013   0.001   PHE B   3 
 TRP   0.012   0.001   TRP B 395 
 HIS   0.002   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5156)
  covalent geometry    : angle       0.51849 ( 6991)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.33115 (    2)
  hydrogen bonds       : bond        0.04150 (  349)
  hydrogen bonds       : angle       3.78005 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.124 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9078 (mtm110) cc_final: 0.8784 (mtm110)
REVERT: B  272 TYR cc_start: 0.9136 (m-80) cc_final: 0.8369 (m-80)
REVERT: B  426 SER cc_start: 0.8847 (m) cc_final: 0.8617 (p)
REVERT: B  468 ARG cc_start: 0.8389 (tmt170) cc_final: 0.6621 (mtt180)
REVERT: B  511 PHE cc_start: 0.9064 (t80) cc_final: 0.8759 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0730
  time to fit residues: 5.7127
Evaluate side-chains
  56 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0870
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0970
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.3756

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.138882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.100331 restraints weight = 6832.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.97
r_work: 0.2955 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5157  Z= 0.106
  Angle     :  0.480   7.529   6993  Z= 0.254
  Chirality :  0.038   0.141    762
  Planarity :  0.004   0.050    869
  Dihedral  :  4.289  27.888    661
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.20 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.36), residues: 598
  helix:  2.46 (0.24), residues: 442
  sheet:  None (None), residues: 0
  loop : -2.55 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 472 
 TYR   0.013   0.001   TYR B 352 
 PHE   0.012   0.001   PHE B   3 
 TRP   0.019   0.001   TRP B 514 
 HIS   0.001   0.000   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5156)
  covalent geometry    : angle       0.47993 ( 6991)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.35902 (    2)
  hydrogen bonds       : bond        0.03622 (  349)
  hydrogen bonds       : angle       3.65669 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.197 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8773 (mtm110)
REVERT: B  215 MET cc_start: 0.8934 (mmm) cc_final: 0.8670 (mmm)
REVERT: B  272 TYR cc_start: 0.9109 (m-80) cc_final: 0.8309 (m-80)
REVERT: B  316 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8762 (mm)
REVERT: B  413 MET cc_start: 0.8652 (ttm) cc_final: 0.8406 (ttm)
REVERT: B  426 SER cc_start: 0.8844 (m) cc_final: 0.8610 (p)
REVERT: B  468 ARG cc_start: 0.8395 (tmt170) cc_final: 0.6651 (mtt180)
REVERT: B  504 HIS cc_start: 0.7752 (t-90) cc_final: 0.7444 (t-90)
  outliers start: 8
  outliers final: 3
  residues processed: 63
  average time/residue: 0.0805
  time to fit residues: 6.6828
Evaluate side-chains
  61 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  575 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0050
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.139830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.101023 restraints weight = 6868.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.96
r_work: 0.2968 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5157  Z= 0.103
  Angle     :  0.472   7.266   6993  Z= 0.248
  Chirality :  0.037   0.122    762
  Planarity :  0.003   0.051    869
  Dihedral  :  4.171  27.140    661
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.57 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.36), residues: 598
  helix:  2.66 (0.24), residues: 443
  sheet:  None (None), residues: 0
  loop : -2.37 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 472 
 TYR   0.014   0.001   TYR B 148 
 PHE   0.012   0.001   PHE B   3 
 TRP   0.015   0.001   TRP B 514 
 HIS   0.002   0.000   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5156)
  covalent geometry    : angle       0.47165 ( 6991)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.33381 (    2)
  hydrogen bonds       : bond        0.03519 (  349)
  hydrogen bonds       : angle       3.57290 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.238 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9093 (mtm110) cc_final: 0.8827 (mtm110)
REVERT: B  171 ARG cc_start: 0.8623 (mtp180) cc_final: 0.8321 (mtp180)
REVERT: B  215 MET cc_start: 0.8951 (mmm) cc_final: 0.8695 (mmm)
REVERT: B  272 TYR cc_start: 0.9119 (m-80) cc_final: 0.8317 (m-80)
REVERT: B  316 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8754 (mm)
REVERT: B  426 SER cc_start: 0.8818 (m) cc_final: 0.8514 (t)
REVERT: B  468 ARG cc_start: 0.8418 (tmt170) cc_final: 0.6678 (mtt180)
REVERT: B  504 HIS cc_start: 0.7672 (t-90) cc_final: 0.7308 (t-90)
REVERT: B  529 ASP cc_start: 0.8614 (m-30) cc_final: 0.8382 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0791
  time to fit residues: 7.2281
Evaluate side-chains
  60 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  346 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
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 = 0.3627 r_free = 0.3627 target = 0.136065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.096012 restraints weight = 7028.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 2.06
r_work: 0.2888 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5157  Z= 0.189
  Angle     :  0.545   7.885   6993  Z= 0.285
  Chirality :  0.041   0.139    762
  Planarity :  0.004   0.059    869
  Dihedral  :  4.282  28.324    661
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.76 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.35), residues: 598
  helix:  2.50 (0.24), residues: 440
  sheet:  None (None), residues: 0
  loop : -2.25 (0.47), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 472 
 TYR   0.012   0.001   TYR B 352 
 PHE   0.012   0.001   PHE B 610 
 TRP   0.025   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 5156)
  covalent geometry    : angle       0.54490 ( 6991)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.29793 (    2)
  hydrogen bonds       : bond        0.04057 (  349)
  hydrogen bonds       : angle       3.68864 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.205 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8900 (mtm110)
REVERT: B  272 TYR cc_start: 0.9174 (m-80) cc_final: 0.8329 (m-80)
REVERT: B  288 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8799 (m-40)
REVERT: B  316 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: B  413 MET cc_start: 0.8702 (ttm) cc_final: 0.8482 (ttm)
REVERT: B  418 SER cc_start: 0.9060 (p) cc_final: 0.8842 (p)
REVERT: B  426 SER cc_start: 0.8778 (m) cc_final: 0.8465 (t)
REVERT: B  468 ARG cc_start: 0.8366 (tmt170) cc_final: 0.6753 (mtt180)
  outliers start: 10
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0657
  time to fit residues: 5.9456
Evaluate side-chains
  65 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  516 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  620 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 479 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.137618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.097458 restraints weight = 6954.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.13
r_work: 0.2900 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5157  Z= 0.135
  Angle     :  0.509   9.290   6993  Z= 0.268
  Chirality :  0.039   0.133    762
  Planarity :  0.004   0.053    869
  Dihedral  :  4.268  28.216    661
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 19.25 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.35), residues: 598
  helix:  2.55 (0.24), residues: 441
  sheet:  None (None), residues: 0
  loop : -2.15 (0.47), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 472 
 TYR   0.012   0.001   TYR B 148 
 PHE   0.016   0.001   PHE B  54 
 TRP   0.027   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 5156)
  covalent geometry    : angle       0.50891 ( 6991)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.31589 (    2)
  hydrogen bonds       : bond        0.03831 (  349)
  hydrogen bonds       : angle       3.65368 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.194 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9159 (mtm110) cc_final: 0.8883 (mtm110)
REVERT: B  171 ARG cc_start: 0.8614 (mtp180) cc_final: 0.8374 (mtp180)
REVERT: B  215 MET cc_start: 0.8956 (mmm) cc_final: 0.8714 (mmm)
REVERT: B  272 TYR cc_start: 0.9150 (m-80) cc_final: 0.8316 (m-80)
REVERT: B  316 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8772 (mm)
REVERT: B  426 SER cc_start: 0.8757 (m) cc_final: 0.8438 (t)
REVERT: B  468 ARG cc_start: 0.8372 (tmt170) cc_final: 0.6619 (mtt180)
REVERT: B  504 HIS cc_start: 0.7401 (t-90) cc_final: 0.7137 (t-90)
  outliers start: 7
  outliers final: 4
  residues processed: 64
  average time/residue: 0.0667
  time to fit residues: 5.7077
Evaluate side-chains
  62 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  620 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.138117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.098138 restraints weight = 7022.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 2.08
r_work: 0.2919 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5157  Z= 0.134
  Angle     :  0.507  10.346   6993  Z= 0.266
  Chirality :  0.039   0.125    762
  Planarity :  0.004   0.055    869
  Dihedral  :  4.262  27.984    661
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.88 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.35), residues: 598
  helix:  2.58 (0.24), residues: 442
  sheet:  None (None), residues: 0
  loop : -2.15 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 472 
 TYR   0.012   0.001   TYR B 148 
 PHE   0.012   0.001   PHE B  54 
 TRP   0.033   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5156)
  covalent geometry    : angle       0.50678 ( 6991)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.31677 (    2)
  hydrogen bonds       : bond        0.03822 (  349)
  hydrogen bonds       : angle       3.65033 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9142 (mtm110) cc_final: 0.8869 (mtm110)
REVERT: B  171 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8320 (mtp180)
REVERT: B  215 MET cc_start: 0.8961 (mmm) cc_final: 0.8719 (mmm)
REVERT: B  272 TYR cc_start: 0.9149 (m-80) cc_final: 0.8329 (m-80)
REVERT: B  316 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: B  426 SER cc_start: 0.8797 (m) cc_final: 0.8496 (t)
REVERT: B  468 ARG cc_start: 0.8407 (tmt170) cc_final: 0.6663 (mtt180)
REVERT: B  504 HIS cc_start: 0.7470 (t-90) cc_final: 0.7131 (t-90)
  outliers start: 11
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0577
  time to fit residues: 4.9437
Evaluate side-chains
  65 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  516 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  620 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.138160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.096258 restraints weight = 6991.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.03
r_work: 0.2920 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5157  Z= 0.137
  Angle     :  0.508  10.570   6993  Z= 0.267
  Chirality :  0.039   0.146    762
  Planarity :  0.003   0.054    869
  Dihedral  :  4.281  27.953    661
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.32 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.35), residues: 598
  helix:  2.60 (0.24), residues: 443
  sheet:  None (None), residues: 0
  loop : -2.10 (0.48), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 371 
 TYR   0.012   0.001   TYR B 148 
 PHE   0.011   0.001   PHE B   3 
 TRP   0.033   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5156)
  covalent geometry    : angle       0.50774 ( 6991)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.33877 (    2)
  hydrogen bonds       : bond        0.03837 (  349)
  hydrogen bonds       : angle       3.66293 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.204 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8876 (mtm110)
REVERT: B  171 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8442 (mtp180)
REVERT: B  215 MET cc_start: 0.8961 (mmm) cc_final: 0.8718 (mmm)
REVERT: B  272 TYR cc_start: 0.9148 (m-80) cc_final: 0.8311 (m-80)
REVERT: B  288 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8744 (m-40)
REVERT: B  316 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8769 (mm)
REVERT: B  426 SER cc_start: 0.8775 (m) cc_final: 0.8481 (t)
REVERT: B  468 ARG cc_start: 0.8408 (tmt170) cc_final: 0.6664 (mtt180)
REVERT: B  504 HIS cc_start: 0.7492 (t-90) cc_final: 0.7155 (t-90)
  outliers start: 12
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0807
  time to fit residues: 6.9563
Evaluate side-chains
  68 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  516 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  620 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0370
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
B 387 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.099023 restraints weight = 6970.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 2.09
r_work: 0.2935 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5157  Z= 0.119
  Angle     :  0.516  11.009   6993  Z= 0.265
  Chirality :  0.038   0.136    762
  Planarity :  0.003   0.054    869
  Dihedral  :  4.246  27.647    661
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 19.63 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.35), residues: 598
  helix:  2.70 (0.24), residues: 442
  sheet:  None (None), residues: 0
  loop : -2.06 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 472 
 TYR   0.012   0.001   TYR B 148 
 PHE   0.016   0.001   PHE B 372 
 TRP   0.035   0.001   TRP B 514 
 HIS   0.001   0.000   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5156)
  covalent geometry    : angle       0.51629 ( 6991)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.37585 (    2)
  hydrogen bonds       : bond        0.03697 (  349)
  hydrogen bonds       : angle       3.64572 ( 1041)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.9186 (mtm110) cc_final: 0.8913 (mtm110)
REVERT: B  215 MET cc_start: 0.8927 (mmm) cc_final: 0.8635 (mmm)
REVERT: B  272 TYR cc_start: 0.9137 (m-80) cc_final: 0.8308 (m-80)
REVERT: B  316 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8760 (mm)
REVERT: B  413 MET cc_start: 0.8560 (ttp) cc_final: 0.8343 (ttm)
REVERT: B  426 SER cc_start: 0.8738 (m) cc_final: 0.8443 (t)
REVERT: B  468 ARG cc_start: 0.8402 (tmt170) cc_final: 0.6670 (mtt180)
REVERT: B  504 HIS cc_start: 0.7336 (t-90) cc_final: 0.7008 (t-90)
  outliers start: 7
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0911
  time to fit residues: 7.7399
Evaluate side-chains
  66 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  516 VAL
Chi-restraints excluded: chain B residue  620 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0570
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.139173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.098702 restraints weight = 7061.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.11
r_work: 0.2933 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5157  Z= 0.125
  Angle     :  0.505  10.700   6993  Z= 0.264
  Chirality :  0.038   0.136    762
  Planarity :  0.004   0.054    869
  Dihedral  :  4.222  27.424    661
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.63 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.36 (0.35), residues: 598
  helix:  2.67 (0.24), residues: 445
  sheet:  None (None), residues: 0
  loop : -2.05 (0.48), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 371 
 TYR   0.012   0.001   TYR B 148 
 PHE   0.033   0.001   PHE B  54 
 TRP   0.031   0.001   TRP B 514 
 HIS   0.001   0.000   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5156)
  covalent geometry    : angle       0.50466 ( 6991)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.32185 (    2)
  hydrogen bonds       : bond        0.03705 (  349)
  hydrogen bonds       : angle       3.62365 ( 1041)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1421.42 seconds
wall clock time: 25 minutes 3.12 seconds (1503.12 seconds total)