Starting phenix.real_space_refine
on Tue Feb 11 17:06:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wu0_21901/02_2025/6wu0_21901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wu0_21901/02_2025/6wu0_21901.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wu0_21901/02_2025/6wu0_21901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wu0_21901/02_2025/6wu0_21901.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wu0_21901/02_2025/6wu0_21901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wu0_21901/02_2025/6wu0_21901.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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
-------------------------------------------------------------------------------
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=   0.648
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      20      5.16       5
     C    4090      2.51       5
     N    1097      2.21       5
     O    1133      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6340
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 6340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6340
          Classifications: {'peptide': 854}
          Link IDs: {'PTRANS': 52, 'TRANS': 801}
          Chain breaks: 1
  Time building chain proxies: 4.03, per 1000 atoms: 0.64
  Number of scatterers: 6340
  At special positions: 0
  Unit cell: (89.64, 70.2, 131.76, 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      20     16.00
     O    1133      8.00
     N    1097      7.00
     C    4090      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=0, symmetry=0
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 1 sheets defined
      74.9% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 15
    Processing helix  chain 'B' and resid 18 through 38
    Processing helix  chain 'B' and resid 52 through 66
      removed outlier: 3.538A  pdb=" N   LEU B  58 " --> pdb=" O   LYS B  54 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 70
      removed outlier: 3.711A  pdb=" N   ASN B  70 " --> pdb=" O   PRO B  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 67 through 70'
    Processing helix  chain 'B' and resid 81 through 102
      removed outlier: 4.036A  pdb=" N   ALA B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 120
    Processing helix  chain 'B' and resid 126 through 140
    Processing helix  chain 'B' and resid 140 through 149
    Processing helix  chain 'B' and resid 152 through 171
      removed outlier: 4.107A  pdb=" N   VAL B 166 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      Proline residue:  B 167  - end of helix
      removed outlier: 3.682A  pdb=" N   GLY B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 177
    Processing helix  chain 'B' and resid 178 through 194
    Processing helix  chain 'B' and resid 233 through 247
      removed outlier: 4.156A  pdb=" N   ARG B 241 " --> pdb=" O   SER B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 253
    Processing helix  chain 'B' and resid 261 through 276
      removed outlier: 3.713A  pdb=" N   GLY B 276 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 296
    Processing helix  chain 'B' and resid 298 through 324
      removed outlier: 3.543A  pdb=" N   ILE B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   SER B 304 " --> pdb=" O   ARG B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 332
      No H-bonds generated for 'chain 'B' and resid 330 through 332'
    Processing helix  chain 'B' and resid 333 through 342
      removed outlier: 4.315A  pdb=" N   VAL B 339 " --> pdb=" O   MET B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 360
      removed outlier: 4.239A  pdb=" N   ALA B 346 " --> pdb=" O   GLY B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 374
    Processing helix  chain 'B' and resid 375 through 391
    Processing helix  chain 'B' and resid 397 through 429
      removed outlier: 3.500A  pdb=" N   SER B 401 " --> pdb=" O   TYR B 397 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   LEU B 422 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
      Proline residue:  B 423  - end of helix
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 3.805A  pdb=" N   TYR B 449 " --> pdb=" O   PRO B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 467
      removed outlier: 3.721A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA B 463 " --> pdb=" O   ILE B 459 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   GLY B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 473
      removed outlier: 3.563A  pdb=" N   LEU B 471 " --> pdb=" O   ALA B 468 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA B 473 " --> pdb=" O   PRO B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.521A  pdb=" N   HIS B 483 " --> pdb=" O   ASN B 480 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS B 485 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 498
      removed outlier: 4.491A  pdb=" N   LEU B 495 " --> pdb=" O   SER B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 545 through 561
      removed outlier: 3.719A  pdb=" N   LYS B 549 " --> pdb=" O   ALA B 545 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY B 559 " --> pdb=" O   ALA B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 564
      No H-bonds generated for 'chain 'B' and resid 562 through 564'
    Processing helix  chain 'B' and resid 573 through 595
    Processing helix  chain 'B' and resid 599 through 614
      removed outlier: 3.539A  pdb=" N   ALA B 603 " --> pdb=" O   GLY B 599 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA B 614 " --> pdb=" O   LEU B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 644
      removed outlier: 3.538A  pdb=" N   GLU B 622 " --> pdb=" O   ALA B 618 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   VAL B 630 " --> pdb=" O   HIS B 626 " (cutoff:3.500A)
      Proline residue:  B 631  - end of helix
      removed outlier: 3.831A  pdb=" N   GLN B 644 " --> pdb=" O   ALA B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 649 through 653
    Processing helix  chain 'B' and resid 654 through 662
      removed outlier: 3.511A  pdb=" N   VAL B 658 " --> pdb=" O   PRO B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 699
      removed outlier: 3.671A  pdb=" N   LEU B 688 " --> pdb=" O   ASP B 684 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 708
    Processing helix  chain 'B' and resid 709 through 739
      removed outlier: 3.586A  pdb=" N   ALA B 713 " --> pdb=" O   ILE B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 741 through 767
      removed outlier: 4.126A  pdb=" N   VAL B 745 " --> pdb=" O   ARG B 741 " (cutoff:3.500A)
      Proline residue:  B 751  - end of helix
    Processing helix  chain 'B' and resid 776 through 796
      removed outlier: 3.887A  pdb=" N   MET B 794 " --> pdb=" O   VAL B 790 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 797 through 799
      No H-bonds generated for 'chain 'B' and resid 797 through 799'
    Processing helix  chain 'B' and resid 809 through 828
    Processing helix  chain 'B' and resid 831 through 854
      removed outlier: 4.311A  pdb=" N   MET B 837 " --> pdb=" O   GLY B 833 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE B 850 " --> pdb=" O   SER B 846 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 855 through 859
    Processing sheet with id=AA1, first strand: chain 'B' and resid 108 through 109
      removed outlier: 3.715A  pdb=" N   ALA B 215 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)

    436 hydrogen bonds defined for protein.
    1272 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: 2.04

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2079
        1.34 -     1.46: 748
        1.46 -     1.57: 3601
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 6466
  Sorted by residual:
  bond pdb=" C   VAL B 858 "
       pdb=" O   VAL B 858 "
    ideal  model  delta    sigma   weight residual
    1.236  1.224  0.012 1.19e-02 7.06e+03 1.05e+00
  bond pdb=" CA  VAL B 670 "
       pdb=" CB  VAL B 670 "
    ideal  model  delta    sigma   weight residual
    1.533  1.545 -0.012 1.26e-02 6.30e+03 8.78e-01
  bond pdb=" CA  VAL B 858 "
       pdb=" C   VAL B 858 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.27e-02 6.20e+03 6.54e-01
  bond pdb=" C   GLU B 213 "
       pdb=" N   PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 2.34e-02 1.83e+03 5.68e-01
  bond pdb=" C   THR B 260 "
       pdb=" N   GLY B 261 "
    ideal  model  delta    sigma   weight residual
    1.331  1.320  0.011 1.46e-02 4.69e+03 5.56e-01
  ... (remaining 6461 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 8607
        1.71 -     3.42: 177
        3.42 -     5.14: 34
        5.14 -     6.85: 10
        6.85 -     8.56: 2
  Bond angle restraints: 8830
  Sorted by residual:
  angle pdb=" C   ASP B 665 "
        pdb=" N   GLY B 666 "
        pdb=" CA  GLY B 666 "
      ideal   model   delta    sigma   weight residual
     121.41  127.46   -6.05 1.96e+00 2.60e-01 9.51e+00
  angle pdb=" C   VAL B 750 "
        pdb=" CA  VAL B 750 "
        pdb=" CB  VAL B 750 "
      ideal   model   delta    sigma   weight residual
     113.70  110.92    2.78 9.50e-01 1.11e+00 8.54e+00
  angle pdb=" C   LEU B 749 "
        pdb=" N   VAL B 750 "
        pdb=" CA  VAL B 750 "
      ideal   model   delta    sigma   weight residual
     120.43  123.12   -2.69 9.60e-01 1.09e+00 7.83e+00
  angle pdb=" CA  LEU B 498 "
        pdb=" CB  LEU B 498 "
        pdb=" CG  LEU B 498 "
      ideal   model   delta    sigma   weight residual
     116.30  124.86   -8.56 3.50e+00 8.16e-02 5.98e+00
  angle pdb=" N   ARG B 740 "
        pdb=" CA  ARG B 740 "
        pdb=" C   ARG B 740 "
      ideal   model   delta    sigma   weight residual
     110.80  115.94   -5.14 2.13e+00 2.20e-01 5.83e+00
  ... (remaining 8825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 3480
       16.09 -    32.18: 328
       32.18 -    48.27: 80
       48.27 -    64.36: 13
       64.36 -    80.45: 3
  Dihedral angle restraints: 3904
    sinusoidal: 1447
      harmonic: 2457
  Sorted by residual:
  dihedral pdb=" CA  GLY B 666 "
           pdb=" C   GLY B 666 "
           pdb=" N   ARG B 667 "
           pdb=" CA  ARG B 667 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.88  -25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  ARG B 667 "
           pdb=" C   ARG B 667 "
           pdb=" N   ALA B 668 "
           pdb=" CA  ALA B 668 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.48  -20.52     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  LEU B 739 "
           pdb=" C   LEU B 739 "
           pdb=" N   ARG B 740 "
           pdb=" CA  ARG B 740 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.17  -18.83     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 3901 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 836
       0.045 -    0.090: 197
       0.090 -    0.134: 54
       0.134 -    0.179: 0
       0.179 -    0.224: 1
  Chirality restraints: 1088
  Sorted by residual:
  chirality pdb=" CB  ILE B 662 "
            pdb=" CA  ILE B 662 "
            pdb=" CG1 ILE B 662 "
            pdb=" CG2 ILE B 662 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CG  LEU B 804 "
            pdb=" CB  LEU B 804 "
            pdb=" CD1 LEU B 804 "
            pdb=" CD2 LEU B 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CA  ILE B 542 "
            pdb=" N   ILE B 542 "
            pdb=" C   ILE B 542 "
            pdb=" CB  ILE B 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1085 not shown)

  Planarity restraints: 1123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 572 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO B 573 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 573 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 573 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 440 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.43e+00
        pdb=" N   PRO B 441 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 441 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 441 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 513 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.76e+00
        pdb=" N   PRO B 514 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 514 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 514 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1120 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 799
        2.75 -     3.29: 6708
        3.29 -     3.82: 10517
        3.82 -     4.36: 11236
        4.36 -     4.90: 19392
  Nonbonded interactions: 48652
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 167 "
            pdb=" OG  SER B 170 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER B 829 "
            pdb=" OG1 THR B 834 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   PHE B 392 "
            pdb=" OG1 THR B 395 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ARG B  98 "
            pdb=" NH1 ARG B  98 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   PRO B 151 "
            pdb=" OG  SER B 629 "
     model   vdw
     2.298 3.040
  ... (remaining 48647 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 group one per residue
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:             0.720
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     19.200
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6274
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   0.023   6466  Z= 0.170
  Angle     :  0.647   8.562   8830  Z= 0.342
  Chirality :  0.040   0.224   1088
  Planarity :  0.004   0.040   1123
  Dihedral  : 13.427  80.447   2308
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.27), residues: 850
  helix: -0.45 (0.20), residues: 562
  sheet: -1.69 (0.88), residues: 38
  loop : -2.89 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  12 
 HIS   0.002   0.001   HIS B 810 
 PHE   0.011   0.001   PHE B 270 
 TYR   0.011   0.001   TYR B 353 
 ARG   0.002   0.000   ARG B 525 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  104 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6873 (mtt90)
REVERT: B  216 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.6619 (mtm-85)
REVERT: B  492 MET cc_start: 0.6525 (ptm) cc_final: 0.6195 (ptm)
REVERT: B  632 LEU cc_start: 0.8448 (tp) cc_final: 0.8048 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1989
  time to fit residues: 39.0592
Evaluate side-chains
  124 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0270
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0980
   chunk 40 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.2244

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B  70 ASN
B 222 GLN
B 474 HIS
B 483 HIS
B 548 GLN
B 656 GLN
B 722 GLN
B 831 HIS
B 856 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.235577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.213565 restraints weight = 9049.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.218179 restraints weight = 5338.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.221383 restraints weight = 3490.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6228
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6466  Z= 0.168
  Angle     :  0.637   7.400   8830  Z= 0.312
  Chirality :  0.041   0.191   1088
  Planarity :  0.005   0.067   1123
  Dihedral  :  4.122  21.379    906
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.18 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.29), residues: 850
  helix:  0.51 (0.21), residues: 594
  sheet: -0.74 (0.93), residues: 38
  loop : -2.85 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 827 
 HIS   0.002   0.001   HIS B  37 
 PHE   0.020   0.001   PHE B 389 
 TYR   0.008   0.001   TYR B 353 
 ARG   0.009   0.000   ARG B 839 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5161 (t-90)
REVERT: B   38 HIS cc_start: 0.6841 (m-70) cc_final: 0.5793 (m-70)
REVERT: B  324 VAL cc_start: 0.8483 (p) cc_final: 0.7931 (m)
REVERT: B  492 MET cc_start: 0.7400 (ptm) cc_final: 0.6967 (ptm)
REVERT: B  766 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7062 (tt)
REVERT: B  794 MET cc_start: 0.4719 (mtp) cc_final: 0.4478 (mtm)
REVERT: B  808 LEU cc_start: 0.5706 (mp) cc_final: 0.4594 (mt)
REVERT: B  827 TRP cc_start: 0.7156 (t60) cc_final: 0.6749 (t60)
REVERT: B  839 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7476 (ttp-110)
  outliers start: 14
  outliers final: 5
  residues processed: 135
  average time/residue: 0.1697
  time to fit residues: 30.8771
Evaluate side-chains
  129 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 5 optimal weight:   30.0000
   chunk 73 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    3.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.234671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.213897 restraints weight = 8753.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.218095 restraints weight = 5219.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.221028 restraints weight = 3451.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6275
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6466  Z= 0.202
  Angle     :  0.655   7.780   8830  Z= 0.322
  Chirality :  0.041   0.160   1088
  Planarity :  0.005   0.053   1123
  Dihedral  :  4.174  24.317    906
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.62 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.30), residues: 850
  helix:  0.85 (0.22), residues: 583
  sheet: -0.55 (0.94), residues: 38
  loop : -2.69 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 827 
 HIS   0.006   0.001   HIS B  37 
 PHE   0.013   0.001   PHE B 720 
 TYR   0.007   0.001   TYR B 353 
 ARG   0.003   0.000   ARG B 621 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5795 (OUTLIER) cc_final: 0.5349 (t-90)
REVERT: B   38 HIS cc_start: 0.6962 (m-70) cc_final: 0.6522 (m-70)
REVERT: B   62 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7151 (tt)
REVERT: B  104 ARG cc_start: 0.7806 (mtt90) cc_final: 0.6607 (mtt90)
REVERT: B  380 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5990 (tt)
REVERT: B  492 MET cc_start: 0.7390 (ptm) cc_final: 0.6942 (ptm)
REVERT: B  499 LYS cc_start: 0.8324 (tttp) cc_final: 0.7999 (tptp)
REVERT: B  656 GLN cc_start: 0.7166 (tp-100) cc_final: 0.6201 (tp-100)
REVERT: B  660 ASP cc_start: 0.7316 (m-30) cc_final: 0.6936 (m-30)
REVERT: B  671 GLN cc_start: 0.7960 (tt0) cc_final: 0.7585 (tt0)
REVERT: B  766 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7316 (tt)
REVERT: B  794 MET cc_start: 0.4748 (mtp) cc_final: 0.4494 (mtm)
REVERT: B  808 LEU cc_start: 0.5857 (mp) cc_final: 0.4731 (mt)
REVERT: B  827 TRP cc_start: 0.7273 (t60) cc_final: 0.6959 (t60)
REVERT: B  839 ARG cc_start: 0.7767 (ttp-110) cc_final: 0.7483 (ttp-110)
  outliers start: 19
  outliers final: 9
  residues processed: 134
  average time/residue: 0.1886
  time to fit residues: 34.5007
Evaluate side-chains
  131 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 28 optimal weight:   40.0000
   chunk 29 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 21 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    4.6588

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.231203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.209045 restraints weight = 9184.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.213344 restraints weight = 5535.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.216368 restraints weight = 3724.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6368
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6466  Z= 0.242
  Angle     :  0.680   7.919   8830  Z= 0.338
  Chirality :  0.042   0.151   1088
  Planarity :  0.005   0.049   1123
  Dihedral  :  4.339  25.811    906
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 19.21 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.30), residues: 850
  helix:  0.93 (0.22), residues: 578
  sheet: -0.78 (0.90), residues: 38
  loop : -2.64 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 827 
 HIS   0.013   0.001   HIS B  37 
 PHE   0.016   0.001   PHE B 720 
 TYR   0.012   0.002   TYR B 353 
 ARG   0.004   0.000   ARG B  98 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.1123 (tt)
REVERT: B   37 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5397 (t-90)
REVERT: B   38 HIS cc_start: 0.7065 (m-70) cc_final: 0.6323 (m-70)
REVERT: B   62 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7365 (tt)
REVERT: B  222 GLN cc_start: 0.7667 (pp30) cc_final: 0.7438 (pp30)
REVERT: B  380 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6117 (tt)
REVERT: B  492 MET cc_start: 0.7375 (ptm) cc_final: 0.6930 (ptm)
REVERT: B  656 GLN cc_start: 0.7196 (tp-100) cc_final: 0.6413 (tp-100)
REVERT: B  660 ASP cc_start: 0.7402 (m-30) cc_final: 0.6947 (m-30)
REVERT: B  671 GLN cc_start: 0.8087 (tt0) cc_final: 0.7765 (tt0)
REVERT: B  766 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7326 (tt)
REVERT: B  794 MET cc_start: 0.4933 (mtp) cc_final: 0.4565 (mtm)
REVERT: B  827 TRP cc_start: 0.7367 (t60) cc_final: 0.7108 (t60)
REVERT: B  839 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7510 (ttp-110)
  outliers start: 29
  outliers final: 17
  residues processed: 138
  average time/residue: 0.1786
  time to fit residues: 33.3450
Evaluate side-chains
  137 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  731 ILE
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  784 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  854 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 43 optimal weight:    9.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 474 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.231590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.209444 restraints weight = 9071.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.213702 restraints weight = 5462.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.216720 restraints weight = 3693.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6466  Z= 0.214
  Angle     :  0.677   7.856   8830  Z= 0.331
  Chirality :  0.043   0.168   1088
  Planarity :  0.005   0.048   1123
  Dihedral  :  4.360  25.022    906
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 20.88 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.30), residues: 850
  helix:  1.11 (0.22), residues: 571
  sheet: -0.85 (0.88), residues: 38
  loop : -2.57 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 827 
 HIS   0.010   0.001   HIS B  37 
 PHE   0.016   0.001   PHE B 720 
 TYR   0.012   0.001   TYR B 353 
 ARG   0.005   0.000   ARG B 212 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 116
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5452 (t-90)
REVERT: B   38 HIS cc_start: 0.7160 (m-70) cc_final: 0.6481 (m-70)
REVERT: B   62 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7337 (tt)
REVERT: B  222 GLN cc_start: 0.7633 (pp30) cc_final: 0.7372 (pp30)
REVERT: B  380 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6059 (tt)
REVERT: B  486 ASP cc_start: 0.7682 (t0) cc_final: 0.7395 (t0)
REVERT: B  492 MET cc_start: 0.7434 (ptm) cc_final: 0.6954 (ptm)
REVERT: B  766 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7243 (tt)
REVERT: B  794 MET cc_start: 0.4909 (mtp) cc_final: 0.4531 (mtm)
REVERT: B  827 TRP cc_start: 0.7308 (t60) cc_final: 0.7025 (t60)
REVERT: B  839 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7638 (ttp-110)
  outliers start: 35
  outliers final: 20
  residues processed: 136
  average time/residue: 0.1799
  time to fit residues: 32.8873
Evaluate side-chains
  140 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  731 ILE
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  784 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  854 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 75 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0170
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    3.1824

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.230283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.208720 restraints weight = 9036.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.212900 restraints weight = 5499.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.215817 restraints weight = 3734.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6466  Z= 0.206
  Angle     :  0.679   9.018   8830  Z= 0.329
  Chirality :  0.042   0.148   1088
  Planarity :  0.005   0.045   1123
  Dihedral  :  4.347  25.538    906
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 22.26 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.30), residues: 850
  helix:  1.20 (0.22), residues: 569
  sheet: -0.86 (0.85), residues: 38
  loop : -2.58 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 827 
 HIS   0.012   0.001   HIS B  37 
 PHE   0.018   0.001   PHE B 720 
 TYR   0.012   0.001   TYR B 353 
 ARG   0.004   0.000   ARG B  98 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5993 (OUTLIER) cc_final: 0.5391 (t-90)
REVERT: B   38 HIS cc_start: 0.7160 (m-70) cc_final: 0.6447 (m-70)
REVERT: B   62 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7370 (tt)
REVERT: B   71 GLN cc_start: 0.7660 (pm20) cc_final: 0.7452 (pm20)
REVERT: B  374 MET cc_start: 0.5612 (mmm) cc_final: 0.5397 (mpp)
REVERT: B  380 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6083 (tt)
REVERT: B  486 ASP cc_start: 0.7695 (t0) cc_final: 0.7491 (t0)
REVERT: B  492 MET cc_start: 0.7377 (ptm) cc_final: 0.6916 (ptm)
REVERT: B  660 ASP cc_start: 0.7410 (m-30) cc_final: 0.6982 (m-30)
REVERT: B  766 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7235 (tt)
REVERT: B  794 MET cc_start: 0.4888 (mtp) cc_final: 0.4488 (mtm)
REVERT: B  827 TRP cc_start: 0.7401 (t60) cc_final: 0.7162 (t60)
  outliers start: 32
  outliers final: 22
  residues processed: 138
  average time/residue: 0.1696
  time to fit residues: 31.3801
Evaluate side-chains
  146 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  731 ILE
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  784 VAL
Chi-restraints excluded: chain B residue  793 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  854 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0980
   chunk 10 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    3.4186

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 274 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.230616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.210118 restraints weight = 9093.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.214538 restraints weight = 5039.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.217412 restraints weight = 3165.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6466  Z= 0.215
  Angle     :  0.700   9.491   8830  Z= 0.340
  Chirality :  0.043   0.196   1088
  Planarity :  0.005   0.045   1123
  Dihedral  :  4.416  24.893    906
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 23.48 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.30), residues: 850
  helix:  1.18 (0.22), residues: 570
  sheet: -0.88 (0.83), residues: 38
  loop : -2.52 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 827 
 HIS   0.005   0.001   HIS B  37 
 PHE   0.030   0.002   PHE B 389 
 TYR   0.012   0.001   TYR B 353 
 ARG   0.005   0.000   ARG B  98 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5749 (OUTLIER) cc_final: 0.5279 (t-90)
REVERT: B   38 HIS cc_start: 0.7077 (m-70) cc_final: 0.6526 (m-70)
REVERT: B  104 ARG cc_start: 0.7794 (mtt90) cc_final: 0.6936 (mtt90)
REVERT: B  380 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6175 (tt)
REVERT: B  486 ASP cc_start: 0.7757 (t0) cc_final: 0.7527 (t0)
REVERT: B  492 MET cc_start: 0.7416 (ptm) cc_final: 0.6944 (ptm)
REVERT: B  660 ASP cc_start: 0.7384 (m-30) cc_final: 0.7012 (m-30)
REVERT: B  766 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7227 (tt)
REVERT: B  794 MET cc_start: 0.4817 (mtp) cc_final: 0.4426 (mtm)
REVERT: B  827 TRP cc_start: 0.7398 (t60) cc_final: 0.7191 (t60)
  outliers start: 33
  outliers final: 25
  residues processed: 137
  average time/residue: 0.1618
  time to fit residues: 30.1121
Evaluate side-chains
  145 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  731 ILE
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  784 VAL
Chi-restraints excluded: chain B residue  793 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  854 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 28 optimal weight:   40.0000
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B  38 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.229632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.208120 restraints weight = 9050.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.212365 restraints weight = 5485.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.215297 restraints weight = 3698.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6466  Z= 0.227
  Angle     :  0.710   9.990   8830  Z= 0.346
  Chirality :  0.043   0.201   1088
  Planarity :  0.005   0.044   1123
  Dihedral  :  4.471  24.781    906
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 24.54 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.30), residues: 850
  helix:  1.10 (0.22), residues: 574
  sheet: -0.88 (0.82), residues: 38
  loop : -2.58 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 827 
 HIS   0.004   0.001   HIS B  37 
 PHE   0.026   0.001   PHE B 389 
 TYR   0.012   0.001   TYR B 353 
 ARG   0.006   0.000   ARG B 839 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5828 (OUTLIER) cc_final: 0.5402 (t-90)
REVERT: B   38 HIS cc_start: 0.7013 (m90) cc_final: 0.6580 (m-70)
REVERT: B  374 MET cc_start: 0.5102 (mmm) cc_final: 0.4610 (mmt)
REVERT: B  380 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6061 (tt)
REVERT: B  486 ASP cc_start: 0.7720 (t0) cc_final: 0.7500 (t0)
REVERT: B  492 MET cc_start: 0.7369 (ptm) cc_final: 0.6925 (ptm)
REVERT: B  660 ASP cc_start: 0.7413 (m-30) cc_final: 0.7020 (m-30)
REVERT: B  766 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7357 (tt)
REVERT: B  827 TRP cc_start: 0.7384 (t60) cc_final: 0.7169 (t60)
  outliers start: 31
  outliers final: 25
  residues processed: 138
  average time/residue: 0.1759
  time to fit residues: 32.5315
Evaluate side-chains
  146 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  731 ILE
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  784 VAL
Chi-restraints excluded: chain B residue  793 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  854 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 44 optimal weight:    0.0040
   chunk 40 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0670
   chunk 84 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    2.4134

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.232313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.209659 restraints weight = 9168.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.214360 restraints weight = 5410.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.217569 restraints weight = 3571.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6466  Z= 0.204
  Angle     :  0.702   8.367   8830  Z= 0.342
  Chirality :  0.042   0.146   1088
  Planarity :  0.005   0.041   1123
  Dihedral  :  4.393  25.008    906
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 25.76 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.30), residues: 850
  helix:  1.18 (0.22), residues: 573
  sheet: -0.74 (0.83), residues: 38
  loop : -2.60 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 827 
 HIS   0.004   0.001   HIS B  37 
 PHE   0.023   0.001   PHE B 389 
 TYR   0.010   0.001   TYR B 353 
 ARG   0.007   0.000   ARG B 839 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  374 MET cc_start: 0.5096 (mmm) cc_final: 0.4693 (mmt)
REVERT: B  380 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6053 (tt)
REVERT: B  492 MET cc_start: 0.7254 (ptm) cc_final: 0.6825 (ptm)
REVERT: B  660 ASP cc_start: 0.7345 (m-30) cc_final: 0.6992 (m-30)
REVERT: B  766 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7355 (tt)
REVERT: B  794 MET cc_start: 0.4678 (mtp) cc_final: 0.4255 (mtm)
REVERT: B  827 TRP cc_start: 0.7363 (t60) cc_final: 0.7123 (t60)
  outliers start: 25
  outliers final: 22
  residues processed: 137
  average time/residue: 0.1712
  time to fit residues: 32.0044
Evaluate side-chains
  145 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  793 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  854 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    0.0070
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0050
   chunk 58 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 41 optimal weight:   20.0000
   overall best weight:    2.0018

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

Flipped N/Q/H residues before XYZ refinement:
B 263 GLN
B 722 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.233050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.210846 restraints weight = 9198.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.215494 restraints weight = 5403.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.218773 restraints weight = 3546.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6311
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   0.033   6466  Z= 0.193
  Angle     :  0.708   8.937   8830  Z= 0.342
  Chirality :  0.042   0.147   1088
  Planarity :  0.005   0.040   1123
  Dihedral  :  4.332  24.400    906
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.22 %
    Favored  : 69.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.30), residues: 850
  helix:  1.30 (0.22), residues: 570
  sheet: -0.63 (0.86), residues: 38
  loop : -2.58 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 827 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.022   0.001   PHE B 720 
 TYR   0.009   0.001   TYR B 353 
 ARG   0.006   0.000   ARG B 839 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  380 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5998 (tt)
REVERT: B  492 MET cc_start: 0.7163 (ptm) cc_final: 0.6756 (ptm)
REVERT: B  566 GLN cc_start: 0.7590 (tp40) cc_final: 0.7285 (pt0)
REVERT: B  660 ASP cc_start: 0.7281 (m-30) cc_final: 0.6904 (m-30)
REVERT: B  766 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7263 (tt)
REVERT: B  793 VAL cc_start: 0.6126 (OUTLIER) cc_final: 0.5779 (t)
REVERT: B  794 MET cc_start: 0.4692 (mtp) cc_final: 0.4028 (mtm)
REVERT: B  827 TRP cc_start: 0.7313 (t60) cc_final: 0.7070 (t60)
  outliers start: 26
  outliers final: 21
  residues processed: 137
  average time/residue: 0.1769
  time to fit residues: 32.4696
Evaluate side-chains
  145 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  149 LYS
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain B residue  499 LYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  793 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 84 optimal weight:    0.7980
   chunk 43 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    0.2980
   chunk 1 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
B  38 HIS
B 644 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.232398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.209849 restraints weight = 9307.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.214551 restraints weight = 5450.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.217765 restraints weight = 3569.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6466  Z= 0.210
  Angle     :  0.725   9.591   8830  Z= 0.351
  Chirality :  0.043   0.213   1088
  Planarity :  0.005   0.040   1123
  Dihedral  :  4.374  25.588    906
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 27.44 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.30), residues: 850
  helix:  1.26 (0.22), residues: 573
  sheet: -0.58 (0.88), residues: 38
  loop : -2.49 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 827 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.023   0.002   PHE B 720 
 TYR   0.009   0.001   TYR B 353 
 ARG   0.006   0.000   ARG B 839 

===============================================================================
Job complete
usr+sys time: 2046.39 seconds
wall clock time: 37 minutes 24.65 seconds (2244.65 seconds total)