Starting phenix.real_space_refine
on Thu Jul 24 20:31:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ugc_64136/07_2025/9ugc_64136.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ugc_64136/07_2025/9ugc_64136.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ugc_64136/07_2025/9ugc_64136.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ugc_64136/07_2025/9ugc_64136.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ugc_64136/07_2025/9ugc_64136.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ugc_64136/07_2025/9ugc_64136.cif"
  }
  resolution = 3.52
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.055
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      32      5.16       5
     C    4252      2.51       5
     N    1096      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6606
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 846, 6494
          Classifications: {'peptide': 846}
          Link IDs: {'PTRANS': 33, 'TRANS': 812}
    Chain: "B"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 112
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 4.48, per 1000 atoms: 0.68
  Number of scatterers: 6606
  At special positions: 0
  Unit cell: (94.668, 83.349, 128.625, 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      32     16.00
     O    1226      8.00
     N    1096      7.00
     C    4252      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: 1.56
  Conformation dependent library (CDL) restraints added in 875.7 milliseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      61.0% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 81
      removed outlier: 3.777A  pdb=" N   LEU A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 100
    Processing helix  chain 'A' and resid 110 through 121
      removed outlier: 3.865A  pdb=" N   LYS A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 138
    Processing helix  chain 'A' and resid 140 through 173
    Processing helix  chain 'A' and resid 192 through 196
    Processing helix  chain 'A' and resid 267 through 280
    Processing helix  chain 'A' and resid 284 through 315
    Processing helix  chain 'A' and resid 318 through 334
      removed outlier: 3.975A  pdb=" N   ILE A 332 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL A 334 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 356
    Processing helix  chain 'A' and resid 363 through 371
      removed outlier: 3.944A  pdb=" N   GLU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 420 through 430
    Processing helix  chain 'A' and resid 433 through 441
      removed outlier: 4.306A  pdb=" N   THR A 441 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 488
      removed outlier: 3.705A  pdb=" N   ASP A 487 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 509
    Processing helix  chain 'A' and resid 540 through 550
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.797A  pdb=" N   GLU A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 585
    Processing helix  chain 'A' and resid 593 through 604
    Processing helix  chain 'A' and resid 611 through 625
      removed outlier: 3.614A  pdb=" N   TYR A 616 " --> pdb=" O   PRO A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 637
      No H-bonds generated for 'chain 'A' and resid 635 through 637'
    Processing helix  chain 'A' and resid 638 through 645
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 670 through 713
      removed outlier: 3.649A  pdb=" N   ILE A 674 " --> pdb=" O   GLY A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
      removed outlier: 3.677A  pdb=" N   ALA A 732 " --> pdb=" O   PHE A 728 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   THR A 733 " --> pdb=" O   ALA A 729 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 734 " --> pdb=" O   ASP A 730 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA A 735 " --> pdb=" O   VAL A 731 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA A 737 " --> pdb=" O   THR A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 779
      removed outlier: 3.767A  pdb=" N   LEU A 779 " --> pdb=" O   THR A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 805
    Processing helix  chain 'A' and resid 805 through 811
      removed outlier: 3.613A  pdb=" N   ILE A 809 " --> pdb=" O   TRP A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 843
    Processing helix  chain 'A' and resid 851 through 878
      removed outlier: 3.637A  pdb=" N   THR A 878 " --> pdb=" O   TYR A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 888
      removed outlier: 3.623A  pdb=" N   ASP A 883 " --> pdb=" O   SER A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 918
      removed outlier: 4.059A  pdb=" N   THR A 918 " --> pdb=" O   HIS A 914 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
    Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 184
    Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 204
      removed outlier: 7.157A  pdb=" N   ASP A 213 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239
    Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 360
      removed outlier: 6.392A  pdb=" N   ALA A 650 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE A 649 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   MET A 631 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 630 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   THR A 632 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   CYS A 376 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   PHE A 607 " --> pdb=" O   VAL A 554 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   MET A 556 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390
      removed outlier: 7.574A  pdb=" N   TRP A 524 " --> pdb=" O   ARG A 519 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ARG A 519 " --> pdb=" O   TRP A 524 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   ILE A 526 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ARG A 517 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY A 528 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   LYS A 457 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   THR A 459 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE A 448 " --> pdb=" O   THR A 459 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL A 461 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1224 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: 2.30

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2141
        1.35 -     1.46: 1504
        1.46 -     1.58: 3039
        1.58 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 6739
  Sorted by residual:
  bond pdb=" N   LEU A  88 "
       pdb=" CA  LEU A  88 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 1.22e-02 6.72e+03 5.90e+00
  bond pdb=" N   LEU A 300 "
       pdb=" CA  LEU A 300 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.96e+00
  bond pdb=" CB  ARG A  97 "
       pdb=" CG  ARG A  97 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.37e+00
  bond pdb=" N   ASN A 178 "
       pdb=" CA  ASN A 178 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.29e-02 6.01e+03 2.17e+00
  bond pdb=" CB  VAL A 723 "
       pdb=" CG2 VAL A 723 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  ... (remaining 6734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 9054
        2.54 -     5.08: 81
        5.08 -     7.62: 12
        7.62 -    10.17: 3
       10.17 -    12.71: 1
  Bond angle restraints: 9151
  Sorted by residual:
  angle pdb=" CB  ARG A  97 "
        pdb=" CG  ARG A  97 "
        pdb=" CD  ARG A  97 "
      ideal   model   delta    sigma   weight residual
     111.30  124.01  -12.71 2.30e+00 1.89e-01 3.05e+01
  angle pdb=" CA  ARG A  97 "
        pdb=" CB  ARG A  97 "
        pdb=" CG  ARG A  97 "
      ideal   model   delta    sigma   weight residual
     114.10  124.13  -10.03 2.00e+00 2.50e-01 2.51e+01
  angle pdb=" CB  MET A 105 "
        pdb=" CG  MET A 105 "
        pdb=" SD  MET A 105 "
      ideal   model   delta    sigma   weight residual
     112.70  122.76  -10.06 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" C   ASN A 178 "
        pdb=" CA  ASN A 178 "
        pdb=" CB  ASN A 178 "
      ideal   model   delta    sigma   weight residual
     110.42  115.96   -5.54 1.99e+00 2.53e-01 7.75e+00
  angle pdb=" CA  LEU A 223 "
        pdb=" CB  LEU A 223 "
        pdb=" CG  LEU A 223 "
      ideal   model   delta    sigma   weight residual
     116.30  126.04   -9.74 3.50e+00 8.16e-02 7.74e+00
  ... (remaining 9146 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3475
       17.95 -    35.89: 412
       35.89 -    53.84: 85
       53.84 -    71.78: 18
       71.78 -    89.73: 11
  Dihedral angle restraints: 4001
    sinusoidal: 1548
      harmonic: 2453
  Sorted by residual:
  dihedral pdb=" CA  THR A 245 "
           pdb=" C   THR A 245 "
           pdb=" N   PHE A 246 "
           pdb=" CA  PHE A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.67  -19.33     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  ASP B  41 "
           pdb=" CB  ASP B  41 "
           pdb=" CG  ASP B  41 "
           pdb=" OD1 ASP B  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.96   56.96     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CB  GLU A 901 "
           pdb=" CG  GLU A 901 "
           pdb=" CD  GLU A 901 "
           pdb=" OE1 GLU A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.42   88.42     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 729
       0.039 -    0.077: 259
       0.077 -    0.116: 65
       0.116 -    0.155: 12
       0.155 -    0.193: 3
  Chirality restraints: 1068
  Sorted by residual:
  chirality pdb=" CA  LEU A 300 "
            pdb=" N   LEU A 300 "
            pdb=" C   LEU A 300 "
            pdb=" CB  LEU A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.35e-01
  chirality pdb=" CG  LEU A 427 "
            pdb=" CB  LEU A 427 "
            pdb=" CD1 LEU A 427 "
            pdb=" CD2 LEU A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.57e-01
  chirality pdb=" CB  VAL A 197 "
            pdb=" CA  VAL A 197 "
            pdb=" CG1 VAL A 197 "
            pdb=" CG2 VAL A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1065 not shown)

  Planarity restraints: 1160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  87 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.22e+00
        pdb=" C   GLY A  87 "    0.040 2.00e-02 2.50e+03
        pdb=" O   GLY A  87 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A  88 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  73 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO A  74 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 126 "   -0.014 2.00e-02 2.50e+03   1.37e-02 3.27e+00
        pdb=" CG  PHE A 126 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 126 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 126 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 126 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 126 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 126 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1157 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 520
        2.74 -     3.28: 7075
        3.28 -     3.82: 11439
        3.82 -     4.36: 13077
        4.36 -     4.90: 22410
  Nonbonded interactions: 54521
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 296 "
            pdb=" CD1 LEU A 300 "
     model   vdw
     2.197 3.460
  nonbonded pdb=" NE1 TRP A 805 "
            pdb=" OD2 ASP A 833 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   ILE A 366 "
            pdb=" OG  SER A 681 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" ND1 HIS A 285 "
            pdb=" OE2 GLU A 367 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   SER A 770 "
            pdb=" OG1 THR A 773 "
     model   vdw
     2.316 3.040
  ... (remaining 54516 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.360
  Find NCS groups from input model:        0.070
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
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   0.046   6739  Z= 0.143
  Angle     :  0.633  12.706   9151  Z= 0.323
  Chirality :  0.042   0.193   1068
  Planarity :  0.004   0.053   1160
  Dihedral  : 16.673  89.729   2427
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 25.11 %
    Favored  : 74.47 %
  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:  1.13 (0.30), residues: 856
  helix:  1.64 (0.24), residues: 481
  sheet: -0.67 (0.53), residues: 80
  loop : -0.21 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 524 
 HIS   0.002   0.000   HIS A 686 
 PHE   0.032   0.002   PHE A 126 
 TYR   0.016   0.001   TYR A 874 
 ARG   0.007   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12364 (  418)
  hydrogen bonds       : angle       5.37668 ( 1224)
  covalent geometry    : bond        0.00310 ( 6739)
  covalent geometry    : angle       0.63292 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 112
  average time/residue: 0.1425
  time to fit residues: 23.0842
Evaluate side-chains
  105 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.166464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.129654 restraints weight = 9692.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130098 restraints weight = 8836.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.131885 restraints weight = 7780.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6739  Z= 0.173
  Angle     :  0.563   7.012   9151  Z= 0.290
  Chirality :  0.042   0.147   1068
  Planarity :  0.004   0.047   1160
  Dihedral  :  4.274  40.681    914
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.40 %
    Favored  : 72.77 %
  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:  1.01 (0.29), residues: 856
  helix:  1.66 (0.23), residues: 491
  sheet: -0.76 (0.48), residues: 96
  loop : -0.56 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 524 
 HIS   0.004   0.001   HIS A 701 
 PHE   0.030   0.002   PHE A 126 
 TYR   0.016   0.002   TYR A 691 
 ARG   0.003   0.000   ARG A 682 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  418)
  hydrogen bonds       : angle       4.55373 ( 1224)
  covalent geometry    : bond        0.00408 ( 6739)
  covalent geometry    : angle       0.56327 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7392 (tptt) cc_final: 0.7086 (tptt)
REVERT: A  309 TRP cc_start: 0.6300 (m100) cc_final: 0.6031 (m100)
REVERT: A  443 TYR cc_start: 0.7048 (m-80) cc_final: 0.6665 (m-10)
REVERT: A  542 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7522 (tp-100)
REVERT: A  609 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: B   49 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5978 (tp30)
  outliers start: 20
  outliers final: 12
  residues processed: 126
  average time/residue: 0.1750
  time to fit residues: 32.3485
Evaluate side-chains
  112 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain B residue   49 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0270
   chunk 71 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0370
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.168038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130944 restraints weight = 9604.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132004 restraints weight = 8134.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.133423 restraints weight = 6558.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6739  Z= 0.133
  Angle     :  0.549   9.314   9151  Z= 0.277
  Chirality :  0.041   0.145   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.948  16.408    912
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.55 %
    Favored  : 73.05 %
  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:  0.97 (0.29), residues: 856
  helix:  1.63 (0.23), residues: 492
  sheet: -0.73 (0.49), residues: 97
  loop : -0.59 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 524 
 HIS   0.005   0.001   HIS A 495 
 PHE   0.018   0.001   PHE A 246 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.002   0.000   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03496 (  418)
  hydrogen bonds       : angle       4.39063 ( 1224)
  covalent geometry    : bond        0.00306 ( 6739)
  covalent geometry    : angle       0.54893 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7420 (tptt) cc_final: 0.7134 (tptt)
REVERT: A  443 TYR cc_start: 0.7025 (m-80) cc_final: 0.6744 (m-10)
REVERT: A  542 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7387 (tp-100)
REVERT: A  740 ASN cc_start: 0.7480 (t0) cc_final: 0.7262 (t0)
REVERT: A  844 TRP cc_start: 0.7447 (m-10) cc_final: 0.5521 (m100)
  outliers start: 24
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1513
  time to fit residues: 28.2903
Evaluate side-chains
  123 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  853 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0970
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.167568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.129943 restraints weight = 9843.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.131078 restraints weight = 8629.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132186 restraints weight = 6439.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6739  Z= 0.132
  Angle     :  0.534   6.401   9151  Z= 0.270
  Chirality :  0.041   0.142   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.878  15.279    912
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.97 %
    Favored  : 71.77 %
  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:  1.11 (0.29), residues: 856
  helix:  1.74 (0.23), residues: 491
  sheet: -0.58 (0.49), residues: 96
  loop : -0.56 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 524 
 HIS   0.003   0.001   HIS A 701 
 PHE   0.031   0.002   PHE A 126 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.004   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  418)
  hydrogen bonds       : angle       4.30189 ( 1224)
  covalent geometry    : bond        0.00308 ( 6739)
  covalent geometry    : angle       0.53384 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7366 (tptt) cc_final: 0.7116 (tptt)
REVERT: A  322 ILE cc_start: 0.8461 (mt) cc_final: 0.8246 (mt)
REVERT: A  346 MET cc_start: 0.8423 (mmp) cc_final: 0.8108 (mmp)
REVERT: A  542 GLN cc_start: 0.7626 (tp-100) cc_final: 0.7333 (tp-100)
REVERT: A  609 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7786 (tm-30)
REVERT: A  844 TRP cc_start: 0.7443 (m-10) cc_final: 0.5568 (m100)
  outliers start: 30
  outliers final: 25
  residues processed: 135
  average time/residue: 0.1961
  time to fit residues: 38.9402
Evaluate side-chains
  127 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0570
   chunk 12 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.167210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.129359 restraints weight = 9720.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.129592 restraints weight = 8269.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.131573 restraints weight = 6738.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6739  Z= 0.152
  Angle     :  0.567   7.749   9151  Z= 0.286
  Chirality :  0.042   0.143   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.924  16.946    912
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 24.40 %
    Favored  : 70.64 %
  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:  1.09 (0.29), residues: 856
  helix:  1.72 (0.23), residues: 491
  sheet: -0.58 (0.48), residues: 96
  loop : -0.57 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 524 
 HIS   0.003   0.001   HIS A 701 
 PHE   0.027   0.001   PHE A 246 
 TYR   0.016   0.001   TYR A 691 
 ARG   0.004   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  418)
  hydrogen bonds       : angle       4.32252 ( 1224)
  covalent geometry    : bond        0.00359 ( 6739)
  covalent geometry    : angle       0.56660 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7450 (tptt) cc_final: 0.7128 (tptt)
REVERT: A  322 ILE cc_start: 0.8570 (mt) cc_final: 0.8341 (mt)
REVERT: A  346 MET cc_start: 0.8443 (mmp) cc_final: 0.8111 (mmp)
REVERT: A  542 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7311 (tp-100)
REVERT: A  844 TRP cc_start: 0.7430 (m-10) cc_final: 0.5568 (m100)
  outliers start: 35
  outliers final: 29
  residues processed: 136
  average time/residue: 0.1623
  time to fit residues: 32.0097
Evaluate side-chains
  128 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 8 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 57 optimal weight:    0.0670
   chunk 35 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.167893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.130649 restraints weight = 9734.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132166 restraints weight = 8439.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.133275 restraints weight = 6263.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6739  Z= 0.135
  Angle     :  0.576   9.468   9151  Z= 0.286
  Chirality :  0.041   0.153   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.908  20.593    912
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 25.39 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.17 (0.29), residues: 856
  helix:  1.80 (0.23), residues: 491
  sheet: -0.54 (0.49), residues: 96
  loop : -0.57 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 524 
 HIS   0.002   0.000   HIS A 701 
 PHE   0.034   0.002   PHE A 126 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.004   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  418)
  hydrogen bonds       : angle       4.30026 ( 1224)
  covalent geometry    : bond        0.00319 ( 6739)
  covalent geometry    : angle       0.57569 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 2.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7403 (tptt) cc_final: 0.7079 (tptt)
REVERT: A  322 ILE cc_start: 0.8502 (mt) cc_final: 0.8264 (mt)
REVERT: A  346 MET cc_start: 0.8402 (mmp) cc_final: 0.8087 (mmp)
REVERT: A  444 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8205 (tptp)
REVERT: A  542 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7319 (tp-100)
REVERT: A  609 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7780 (tm-30)
REVERT: A  844 TRP cc_start: 0.7432 (m-10) cc_final: 0.5560 (m100)
  outliers start: 36
  outliers final: 31
  residues processed: 131
  average time/residue: 0.2077
  time to fit residues: 40.6160
Evaluate side-chains
  127 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 48 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.166091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.128958 restraints weight = 9655.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129199 restraints weight = 8060.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.130989 restraints weight = 6899.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6739  Z= 0.159
  Angle     :  0.588   8.759   9151  Z= 0.293
  Chirality :  0.042   0.188   1068
  Planarity :  0.004   0.045   1160
  Dihedral  :  3.935  20.184    912
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 25.25 %
    Favored  : 69.65 %
  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:  1.15 (0.29), residues: 856
  helix:  1.77 (0.23), residues: 492
  sheet: -0.57 (0.50), residues: 96
  loop : -0.57 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 817 
 HIS   0.004   0.001   HIS A 701 
 PHE   0.031   0.002   PHE A 246 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  418)
  hydrogen bonds       : angle       4.29881 ( 1224)
  covalent geometry    : bond        0.00378 ( 6739)
  covalent geometry    : angle       0.58825 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 TRP cc_start: 0.7352 (m-10) cc_final: 0.6696 (m100)
REVERT: A  322 ILE cc_start: 0.8534 (mt) cc_final: 0.8324 (mt)
REVERT: A  346 MET cc_start: 0.8426 (mmp) cc_final: 0.8123 (mmp)
REVERT: A  444 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8231 (tmtt)
REVERT: A  542 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7353 (tp-100)
REVERT: A  844 TRP cc_start: 0.7375 (m-10) cc_final: 0.5488 (m100)
  outliers start: 36
  outliers final: 31
  residues processed: 134
  average time/residue: 0.2354
  time to fit residues: 46.9684
Evaluate side-chains
  133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 63 optimal weight:    0.3980
   chunk 10 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.166176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128665 restraints weight = 9731.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128401 restraints weight = 7790.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130343 restraints weight = 6314.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6739  Z= 0.161
  Angle     :  0.608  11.036   9151  Z= 0.300
  Chirality :  0.042   0.190   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.989  21.543    912
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.38 %
    Favored  : 68.94 %
  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:  1.12 (0.29), residues: 856
  helix:  1.74 (0.23), residues: 490
  sheet: -0.69 (0.48), residues: 101
  loop : -0.48 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 817 
 HIS   0.003   0.001   HIS A 701 
 PHE   0.036   0.002   PHE A 126 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.001   0.000   ARG A 884 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  418)
  hydrogen bonds       : angle       4.29474 ( 1224)
  covalent geometry    : bond        0.00384 ( 6739)
  covalent geometry    : angle       0.60802 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7483 (tptt) cc_final: 0.7119 (tptt)
REVERT: A  322 ILE cc_start: 0.8452 (mt) cc_final: 0.8241 (mt)
REVERT: A  346 MET cc_start: 0.8452 (mmp) cc_final: 0.8152 (mmp)
REVERT: A  444 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8196 (tmtt)
REVERT: A  542 GLN cc_start: 0.7586 (tp-100) cc_final: 0.7370 (tp-100)
REVERT: A  844 TRP cc_start: 0.7384 (m-10) cc_final: 0.5467 (m100)
  outliers start: 33
  outliers final: 31
  residues processed: 131
  average time/residue: 0.1734
  time to fit residues: 33.7723
Evaluate side-chains
  131 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0470
   chunk 2 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 27 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.166417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.128934 restraints weight = 9805.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128867 restraints weight = 8421.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.131099 restraints weight = 6842.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6739  Z= 0.154
  Angle     :  0.609  12.031   9151  Z= 0.301
  Chirality :  0.042   0.181   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.973  20.950    912
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 26.10 %
    Favored  : 68.79 %
  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:  1.08 (0.29), residues: 856
  helix:  1.69 (0.23), residues: 490
  sheet: -0.63 (0.48), residues: 101
  loop : -0.49 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 817 
 HIS   0.004   0.001   HIS A 701 
 PHE   0.028   0.002   PHE A 246 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  418)
  hydrogen bonds       : angle       4.29389 ( 1224)
  covalent geometry    : bond        0.00366 ( 6739)
  covalent geometry    : angle       0.60936 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7457 (tptt) cc_final: 0.7090 (tptt)
REVERT: A  322 ILE cc_start: 0.8472 (mt) cc_final: 0.8254 (mt)
REVERT: A  346 MET cc_start: 0.8465 (mmp) cc_final: 0.8146 (mmp)
REVERT: A  444 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8252 (tmtt)
REVERT: A  542 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7369 (tp-100)
REVERT: A  609 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7231 (tm-30)
REVERT: A  844 TRP cc_start: 0.7346 (m-10) cc_final: 0.5455 (m100)
  outliers start: 36
  outliers final: 32
  residues processed: 130
  average time/residue: 0.1905
  time to fit residues: 35.8880
Evaluate side-chains
  134 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 2.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0870
   chunk 82 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0570
   chunk 83 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.167713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.129324 restraints weight = 9874.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130094 restraints weight = 8353.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132325 restraints weight = 5914.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6739  Z= 0.131
  Angle     :  0.604  12.678   9151  Z= 0.294
  Chirality :  0.042   0.157   1068
  Planarity :  0.004   0.046   1160
  Dihedral  :  3.917  20.079    912
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.52 %
    Favored  : 68.79 %
  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:  1.14 (0.29), residues: 856
  helix:  1.74 (0.23), residues: 490
  sheet: -0.57 (0.49), residues: 101
  loop : -0.47 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 817 
 HIS   0.002   0.000   HIS A 686 
 PHE   0.023   0.001   PHE A 246 
 TYR   0.015   0.001   TYR A 691 
 ARG   0.002   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03186 (  418)
  hydrogen bonds       : angle       4.24411 ( 1224)
  covalent geometry    : bond        0.00308 ( 6739)
  covalent geometry    : angle       0.60373 ( 9151)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 2.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.7440 (tptt) cc_final: 0.7092 (tptt)
REVERT: A  322 ILE cc_start: 0.8457 (mt) cc_final: 0.8202 (mt)
REVERT: A  346 MET cc_start: 0.8431 (mmp) cc_final: 0.8101 (mmp)
REVERT: A  444 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8292 (tmtt)
REVERT: A  542 GLN cc_start: 0.7522 (tp-100) cc_final: 0.7319 (tp-100)
REVERT: A  609 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7184 (tm-30)
REVERT: A  844 TRP cc_start: 0.7226 (m-10) cc_final: 0.5374 (m100)
  outliers start: 33
  outliers final: 28
  residues processed: 133
  average time/residue: 0.2958
  time to fit residues: 57.2499
Evaluate side-chains
  131 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  609 GLU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  647 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  750 TRP
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  897 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0970
   chunk 75 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.167172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.129742 restraints weight = 9745.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.129600 restraints weight = 8807.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.131450 restraints weight = 7315.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6739  Z= 0.156
  Angle     :  0.627  12.517   9151  Z= 0.309
  Chirality :  0.043   0.177   1068
  Planarity :  0.004   0.045   1160
  Dihedral  :  4.003  21.243    912
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 27.09 %
    Favored  : 68.51 %
  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:  1.17 (0.29), residues: 856
  helix:  1.76 (0.23), residues: 489
  sheet: -0.47 (0.52), residues: 93
  loop : -0.50 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 817 
 HIS   0.003   0.001   HIS A 701 
 PHE   0.013   0.001   PHE A 666 
 TYR   0.016   0.001   TYR A 691 
 ARG   0.008   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  418)
  hydrogen bonds       : angle       4.26610 ( 1224)
  covalent geometry    : bond        0.00374 ( 6739)
  covalent geometry    : angle       0.62698 ( 9151)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3213.13 seconds
wall clock time: 61 minutes 13.64 seconds (3673.64 seconds total)