Starting phenix.real_space_refine
on Tue Mar 11 16:37:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wu0_21901/03_2025/6wu0_21901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wu0_21901/03_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_21901/03_2025/6wu0_21901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_2025/6wu0_21901.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_2025/6wu0_21901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.92, per 1000 atoms: 0.62
  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: 1.52
  Conformation dependent library (CDL) restraints added in 894.8 milliseconds
  

  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: 0.63
  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: 1.78

  Time building geometry restraints manager: 1.81 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:             0.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.000
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.340
-------------------------------------------------------------------------------
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  : 0.705 
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: 0.2020
  time to fit residues: 40.3072
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  : 0.692 
-------------------------------------------------------------------------------
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 = 35)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.213563 restraints weight = 9049.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.218112 restraints weight = 5338.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.221338 restraints weight = 3510.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
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  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.5163 (t-90)
REVERT: B   38 HIS cc_start: 0.6841 (m-70) cc_final: 0.5791 (m-70)
REVERT: B  324 VAL cc_start: 0.8481 (p) cc_final: 0.7931 (m)
REVERT: B  492 MET cc_start: 0.7402 (ptm) cc_final: 0.6971 (ptm)
REVERT: B  766 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7061 (tt)
REVERT: B  794 MET cc_start: 0.4720 (mtp) cc_final: 0.4479 (mtm)
REVERT: B  808 LEU cc_start: 0.5706 (mp) cc_final: 0.4595 (mt)
REVERT: B  827 TRP cc_start: 0.7153 (t60) cc_final: 0.6744 (t60)
REVERT: B  839 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7474 (ttp-110)
  outliers start: 14
  outliers final: 5
  residues processed: 135
  average time/residue: 0.1723
  time to fit residues: 31.6121
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  : 0.636 
-------------------------------------------------------------------------------
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:    0.0060
   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:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    3.2002

-------------------------------------------------------------------------------
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 = 0.4430 r_free = 0.4430 target = 0.232639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.211076 restraints weight = 9125.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.215336 restraints weight = 5549.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.218358 restraints weight = 3738.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6283
moved from start:          0.1472

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= 0.209
  Angle     :  0.661   7.808   8830  Z= 0.325
  Chirality :  0.042   0.159   1088
  Planarity :  0.005   0.053   1123
  Dihedral  :  4.187  24.578    906
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  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: -0.57 (0.94), residues: 38
  loop : -2.69 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 827 
 HIS   0.010   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
  145 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5853 (OUTLIER) cc_final: 0.5455 (t-90)
REVERT: B   38 HIS cc_start: 0.6988 (m-70) cc_final: 0.6596 (m-70)
REVERT: B   62 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7159 (tt)
REVERT: B  104 ARG cc_start: 0.7818 (mtt90) cc_final: 0.6591 (mtt90)
REVERT: B  216 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7520 (ptp90)
REVERT: B  380 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5962 (tt)
REVERT: B  492 MET cc_start: 0.7419 (ptm) cc_final: 0.6965 (ptm)
REVERT: B  499 LYS cc_start: 0.8374 (tttp) cc_final: 0.8069 (tptp)
REVERT: B  656 GLN cc_start: 0.7169 (tp-100) cc_final: 0.6192 (tp-100)
REVERT: B  660 ASP cc_start: 0.7322 (m-30) cc_final: 0.6942 (m-30)
REVERT: B  671 GLN cc_start: 0.7965 (tt0) cc_final: 0.7592 (tt0)
REVERT: B  766 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7312 (tt)
REVERT: B  794 MET cc_start: 0.4839 (mtp) cc_final: 0.4578 (mtm)
REVERT: B  808 LEU cc_start: 0.5837 (mp) cc_final: 0.4732 (mt)
REVERT: B  827 TRP cc_start: 0.7254 (t60) cc_final: 0.6925 (t60)
REVERT: B  839 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7459 (ttp-110)
  outliers start: 19
  outliers final: 9
  residues processed: 135
  average time/residue: 0.1753
  time to fit residues: 32.3116
Evaluate side-chains
  132 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 28 optimal weight:   40.0000
   chunk 29 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 75 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    3.1586

-------------------------------------------------------------------------------
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 = 0.4429 r_free = 0.4429 target = 0.232297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.210537 restraints weight = 9195.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.214753 restraints weight = 5550.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.217780 restraints weight = 3733.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6294
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6466  Z= 0.199
  Angle     :  0.651   7.802   8830  Z= 0.319
  Chirality :  0.042   0.156   1088
  Planarity :  0.005   0.048   1123
  Dihedral  :  4.200  24.315    906
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.60 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.01 (0.30), residues: 850
  helix:  1.07 (0.22), residues: 577
  sheet: -0.62 (0.91), residues: 38
  loop : -2.66 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 827 
 HIS   0.011   0.001   HIS B  37 
 PHE   0.016   0.001   PHE B 392 
 TYR   0.010   0.001   TYR B 353 
 ARG   0.003   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
  154 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5891 (OUTLIER) cc_final: 0.5468 (t-90)
REVERT: B   38 HIS cc_start: 0.7044 (m-70) cc_final: 0.6559 (m-70)
REVERT: B   62 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7228 (tt)
REVERT: B  104 ARG cc_start: 0.7797 (mtt90) cc_final: 0.6999 (mtt90)
REVERT: B  216 ARG cc_start: 0.7757 (ptp90) cc_final: 0.7538 (ptp90)
REVERT: B  380 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5987 (tt)
REVERT: B  492 MET cc_start: 0.7383 (ptm) cc_final: 0.6935 (ptm)
REVERT: B  499 LYS cc_start: 0.8406 (tttp) cc_final: 0.8205 (tptp)
REVERT: B  656 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6308 (tp-100)
REVERT: B  660 ASP cc_start: 0.7360 (m-30) cc_final: 0.6924 (m-30)
REVERT: B  671 GLN cc_start: 0.8019 (tt0) cc_final: 0.7650 (tt0)
REVERT: B  766 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7306 (tt)
REVERT: B  794 MET cc_start: 0.4852 (mtp) cc_final: 0.4549 (mtm)
REVERT: B  808 LEU cc_start: 0.5789 (mp) cc_final: 0.5272 (mp)
REVERT: B  827 TRP cc_start: 0.7278 (t60) cc_final: 0.7019 (t60)
REVERT: B  839 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7490 (ttp-110)
  outliers start: 28
  outliers final: 16
  residues processed: 140
  average time/residue: 0.1946
  time to fit residues: 37.1988
Evaluate side-chains
  139 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.4414 r_free = 0.4414 target = 0.230489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.208753 restraints weight = 9081.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.212994 restraints weight = 5518.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.215872 restraints weight = 3735.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6328
moved from start:          0.1794

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= 0.217
  Angle     :  0.668   7.849   8830  Z= 0.328
  Chirality :  0.043   0.178   1088
  Planarity :  0.005   0.069   1123
  Dihedral  :  4.313  24.913    906
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 20.27 %
    Favored  : 75.00 %
  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:  0.07 (0.30), residues: 850
  helix:  1.10 (0.22), residues: 579
  sheet: -0.63 (0.90), residues: 38
  loop : -2.54 (0.41), residues: 233

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
  155 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5512 (t-90)
REVERT: B   38 HIS cc_start: 0.7136 (m-70) cc_final: 0.6528 (m-70)
REVERT: B   62 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7343 (tt)
REVERT: B   71 GLN cc_start: 0.7506 (pm20) cc_final: 0.7291 (pm20)
REVERT: B  104 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7026 (mtt90)
REVERT: B  216 ARG cc_start: 0.7744 (ptp90) cc_final: 0.7536 (ptp90)
REVERT: B  380 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6085 (tt)
REVERT: B  486 ASP cc_start: 0.7610 (t0) cc_final: 0.7320 (t0)
REVERT: B  492 MET cc_start: 0.7395 (ptm) cc_final: 0.6919 (ptm)
REVERT: B  671 GLN cc_start: 0.8129 (tt0) cc_final: 0.7795 (tt0)
REVERT: B  766 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7243 (tt)
REVERT: B  794 MET cc_start: 0.4918 (mtp) cc_final: 0.4579 (mtm)
REVERT: B  827 TRP cc_start: 0.7296 (t60) cc_final: 0.7014 (t60)
REVERT: B  839 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7609 (ttp-110)
  outliers start: 31
  outliers final: 20
  residues processed: 141
  average time/residue: 0.1847
  time to fit residues: 34.8998
Evaluate side-chains
  143 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 75 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:   20.0000
   chunk 66 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0870
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    2.7564

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 805 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.233035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.210886 restraints weight = 9068.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.215220 restraints weight = 5523.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.218234 restraints weight = 3745.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.1937

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= 0.196
  Angle     :  0.675   8.954   8830  Z= 0.325
  Chirality :  0.042   0.186   1088
  Planarity :  0.005   0.057   1123
  Dihedral  :  4.272  24.143    906
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 22.56 %
    Favored  : 72.56 %
  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:  0.26 (0.30), residues: 850
  helix:  1.27 (0.22), residues: 571
  sheet: -0.48 (0.87), residues: 38
  loop : -2.45 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  55 
 HIS   0.005   0.001   HIS B  37 
 PHE   0.018   0.001   PHE B 720 
 TYR   0.011   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
  156 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5301 (t-90)
REVERT: B   38 HIS cc_start: 0.7049 (m-70) cc_final: 0.6493 (m-70)
REVERT: B   62 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7392 (tt)
REVERT: B  380 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6114 (tt)
REVERT: B  492 MET cc_start: 0.7298 (ptm) cc_final: 0.6859 (ptm)
REVERT: B  660 ASP cc_start: 0.7362 (m-30) cc_final: 0.6999 (m-30)
REVERT: B  671 GLN cc_start: 0.8062 (tt0) cc_final: 0.7612 (tt0)
REVERT: B  766 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: B  794 MET cc_start: 0.4932 (mtp) cc_final: 0.4544 (mtm)
REVERT: B  808 LEU cc_start: 0.6062 (mp) cc_final: 0.5290 (mp)
REVERT: B  827 TRP cc_start: 0.7375 (t60) cc_final: 0.7154 (t60)
  outliers start: 32
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1747
  time to fit residues: 32.8218
Evaluate side-chains
  144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
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  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  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  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:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0770
   chunk 10 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0040
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.5752

-------------------------------------------------------------------------------
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
B 722 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.237088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.216205 restraints weight = 8703.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.220416 restraints weight = 5157.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.223406 restraints weight = 3410.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.4346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6215
moved from start:          0.2034

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= 0.170
  Angle     :  0.670   9.875   8830  Z= 0.319
  Chirality :  0.041   0.196   1088
  Planarity :  0.004   0.045   1123
  Dihedral  :  4.153  23.326    906
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 23.78 %
    Favored  : 72.26 %
  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:  0.43 (0.30), residues: 850
  helix:  1.40 (0.22), residues: 574
  sheet: -0.13 (0.89), residues: 38
  loop : -2.50 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 827 
 HIS   0.008   0.001   HIS B  37 
 PHE   0.019   0.001   PHE B 720 
 TYR   0.008   0.001   TYR B 353 
 ARG   0.005   0.000   ARG B 839 

*********************** 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
  153 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5689 (OUTLIER) cc_final: 0.5287 (t-90)
REVERT: B   38 HIS cc_start: 0.7020 (m-70) cc_final: 0.6506 (m-70)
REVERT: B  104 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7003 (mtt90)
REVERT: B  149 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8393 (ttmt)
REVERT: B  178 MET cc_start: 0.6586 (pmm) cc_final: 0.6383 (pmm)
REVERT: B  380 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6057 (tt)
REVERT: B  492 MET cc_start: 0.7225 (ptm) cc_final: 0.6781 (ptm)
REVERT: B  660 ASP cc_start: 0.7327 (m-30) cc_final: 0.6952 (m-30)
REVERT: B  671 GLN cc_start: 0.7853 (tt0) cc_final: 0.7394 (tt0)
REVERT: B  766 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7205 (tt)
REVERT: B  794 MET cc_start: 0.4828 (mtp) cc_final: 0.4474 (mtm)
REVERT: B  808 LEU cc_start: 0.6021 (mp) cc_final: 0.5283 (mp)
REVERT: B  827 TRP cc_start: 0.7391 (t60) cc_final: 0.7149 (t60)
  outliers start: 26
  outliers final: 18
  residues processed: 141
  average time/residue: 0.1761
  time to fit residues: 33.5502
Evaluate side-chains
  143 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  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  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  687 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:   20.0000
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0010
   chunk 35 optimal weight:    8.9990
   chunk 40 optimal weight:   20.0000
   chunk 78 optimal weight:    1.9990
   chunk 28 optimal weight:   40.0000
   chunk 68 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    2.1392

-------------------------------------------------------------------------------
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
** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.234257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.212525 restraints weight = 9102.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.216856 restraints weight = 5539.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.219893 restraints weight = 3730.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6466  Z= 0.196
  Angle     :  0.685   9.511   8830  Z= 0.328
  Chirality :  0.042   0.216   1088
  Planarity :  0.005   0.042   1123
  Dihedral  :  4.170  23.466    906
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 25.30 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.55 (0.30), residues: 850
  helix:  1.42 (0.22), residues: 574
  sheet: -0.18 (0.87), residues: 38
  loop : -2.23 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 827 
 HIS   0.003   0.001   HIS B  37 
 PHE   0.021   0.001   PHE B 720 
 TYR   0.009   0.001   TYR B 353 
 ARG   0.007   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
  148 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.5325 (t-90)
REVERT: B   38 HIS cc_start: 0.6896 (m90) cc_final: 0.6536 (m-70)
REVERT: B  104 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7002 (mtt90)
REVERT: B  380 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6026 (tt)
REVERT: B  492 MET cc_start: 0.7242 (ptm) cc_final: 0.6794 (ptm)
REVERT: B  566 GLN cc_start: 0.7676 (tp40) cc_final: 0.7448 (tp40)
REVERT: B  660 ASP cc_start: 0.7417 (m-30) cc_final: 0.7023 (m-30)
REVERT: B  671 GLN cc_start: 0.7836 (tt0) cc_final: 0.7334 (tt0)
REVERT: B  766 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7227 (tt)
REVERT: B  794 MET cc_start: 0.4805 (mtp) cc_final: 0.4451 (mtm)
REVERT: B  808 LEU cc_start: 0.5958 (mp) cc_final: 0.5245 (mp)
REVERT: B  827 TRP cc_start: 0.7326 (t60) cc_final: 0.7059 (t60)
  outliers start: 25
  outliers final: 20
  residues processed: 136
  average time/residue: 0.1835
  time to fit residues: 34.2747
Evaluate side-chains
  143 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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  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  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  687 MET
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0030
   chunk 3 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    4.7998

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 263 GLN
** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.229141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.207138 restraints weight = 9333.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.211479 restraints weight = 5695.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.214594 restraints weight = 3854.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6466  Z= 0.262
  Angle     :  0.740   9.114   8830  Z= 0.358
  Chirality :  0.044   0.167   1088
  Planarity :  0.005   0.046   1123
  Dihedral  :  4.398  26.658    906
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 25.61 %
    Favored  : 70.27 %
  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:  0.24 (0.30), residues: 850
  helix:  1.17 (0.22), residues: 578
  sheet: -0.48 (0.85), residues: 38
  loop : -2.33 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  55 
 HIS   0.014   0.001   HIS B  37 
 PHE   0.023   0.002   PHE B 720 
 TYR   0.014   0.002   TYR B 353 
 ARG   0.006   0.001   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: 27
    poor density    : 121
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5847 (OUTLIER) cc_final: 0.5228 (t-90)
REVERT: B   38 HIS cc_start: 0.7007 (m90) cc_final: 0.6183 (m-70)
REVERT: B  380 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6153 (tt)
REVERT: B  428 LEU cc_start: 0.4715 (OUTLIER) cc_final: 0.1940 (tp)
REVERT: B  492 MET cc_start: 0.7281 (ptm) cc_final: 0.6861 (ptm)
REVERT: B  660 ASP cc_start: 0.7206 (m-30) cc_final: 0.6845 (m-30)
REVERT: B  746 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6864 (pp)
REVERT: B  766 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7269 (tt)
REVERT: B  827 TRP cc_start: 0.7352 (t60) cc_final: 0.7104 (t60)
  outliers start: 27
  outliers final: 19
  residues processed: 138
  average time/residue: 0.1580
  time to fit residues: 30.2737
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  : 0.693 
-------------------------------------------------------------------------------
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  149 LYS
Chi-restraints excluded: chain B residue  183 SER
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  565 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    0.0030
   chunk 63 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 48 optimal weight:   30.0000
   chunk 43 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 84 optimal weight:    0.3980
   chunk 19 optimal weight:    6.9990
   chunk 41 optimal weight:   20.0000
   overall best weight:    2.2796

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

Flipped N/Q/H residues before XYZ refinement:
B  37 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 = 0.4428 r_free = 0.4428 target = 0.231572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.209013 restraints weight = 9081.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.213788 restraints weight = 5292.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.217040 restraints weight = 3462.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6263
moved from start:          0.2347

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= 0.202
  Angle     :  0.715   9.274   8830  Z= 0.343
  Chirality :  0.042   0.167   1088
  Planarity :  0.005   0.044   1123
  Dihedral  :  4.306  23.711    906
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.52 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.33 (0.30), residues: 850
  helix:  1.31 (0.22), residues: 573
  sheet: -0.33 (0.88), residues: 38
  loop : -2.45 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 827 
 HIS   0.008   0.001   HIS B  37 
 PHE   0.023   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
  150 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.5781 (OUTLIER) cc_final: 0.5192 (t-90)
REVERT: B   38 HIS cc_start: 0.7102 (m90) cc_final: 0.6567 (m-70)
REVERT: B   50 GLU cc_start: 0.8477 (tp30) cc_final: 0.8174 (tp30)
REVERT: B  380 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5967 (tt)
REVERT: B  492 MET cc_start: 0.7356 (ptm) cc_final: 0.6897 (ptm)
REVERT: B  566 GLN cc_start: 0.7688 (tp40) cc_final: 0.7304 (pt0)
REVERT: B  660 ASP cc_start: 0.7318 (m-30) cc_final: 0.6904 (m-30)
REVERT: B  746 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6770 (pp)
REVERT: B  766 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7207 (tt)
REVERT: B  794 MET cc_start: 0.4573 (mtp) cc_final: 0.4143 (mtm)
REVERT: B  827 TRP cc_start: 0.7272 (t60) cc_final: 0.7010 (t60)
  outliers start: 26
  outliers final: 20
  residues processed: 140
  average time/residue: 0.1791
  time to fit residues: 34.3678
Evaluate side-chains
  149 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 VAL
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  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  565 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   chunk 43 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0470
   chunk 11 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.4880

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 263 GLN
B 644 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.234542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.212233 restraints weight = 9214.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.216942 restraints weight = 5394.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.220196 restraints weight = 3528.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6259
moved from start:          0.2415

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= 0.192
  Angle     :  0.708   9.758   8830  Z= 0.339
  Chirality :  0.042   0.161   1088
  Planarity :  0.005   0.042   1123
  Dihedral  :  4.235  23.431    906
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 26.83 %
    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:  0.50 (0.30), residues: 850
  helix:  1.46 (0.22), residues: 570
  sheet: -0.30 (0.88), residues: 38
  loop : -2.37 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 827 
 HIS   0.006   0.001   HIS B  38 
 PHE   0.023   0.001   PHE B 720 
 TYR   0.008   0.001   TYR B 353 
 ARG   0.006   0.000   ARG B 839 

===============================================================================
Job complete
usr+sys time: 2229.15 seconds
wall clock time: 39 minutes 21.83 seconds (2361.83 seconds total)