Starting phenix.real_space_refine
on Fri Jul 25 17:45:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbz_61331/07_2025/9jbz_61331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbz_61331/07_2025/9jbz_61331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbz_61331/07_2025/9jbz_61331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbz_61331/07_2025/9jbz_61331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbz_61331/07_2025/9jbz_61331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbz_61331/07_2025/9jbz_61331.cif"
  }
  resolution = 3.67
  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=   0.003 sd=   0.039
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      47      5.16       5
     C    5131      2.51       5
     N    1334      2.21       5
     O    1436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7948
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1016, 7948
          Classifications: {'peptide': 1016}
          Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 962}
          Chain breaks: 1
  Time building chain proxies: 5.05, per 1000 atoms: 0.64
  Number of scatterers: 7948
  At special positions: 0
  Unit cell: (83.2, 95.68, 145.6, 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      47     16.00
     O    1436      8.00
     N    1334      7.00
     C    5131      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: 2.04
  Conformation dependent library (CDL) restraints added in 956.3 milliseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 8 sheets defined
      51.1% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 130
      removed outlier: 3.589A  pdb=" N   HIS A 123 " --> pdb=" O   HIS A 119 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 124 " --> pdb=" O   TRP A 120 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   HIS A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS A 126 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
      removed outlier: 3.806A  pdb=" N   GLY A 197 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 3.991A  pdb=" N   SER A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 223
    Processing helix  chain 'A' and resid 233 through 243
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 262 through 295
      removed outlier: 3.566A  pdb=" N   GLU A 290 " --> pdb=" O   ARG A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 382
      removed outlier: 3.777A  pdb=" N   HIS A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 378 through 382'
    Processing helix  chain 'A' and resid 417 through 420
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 441 through 468
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.630A  pdb=" N   LEU A 477 " --> pdb=" O   ASN A 473 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 3.990A  pdb=" N   LEU A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 525
      Proline residue:  A 522  - end of helix
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.760A  pdb=" N   THR A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 574
      removed outlier: 3.543A  pdb=" N   CYS A 574 " --> pdb=" O   ALA A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 656 through 663
      removed outlier: 4.510A  pdb=" N   SER A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   MET A 663 " --> pdb=" O   THR A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 681
    Processing helix  chain 'A' and resid 697 through 704
      removed outlier: 3.674A  pdb=" N   ARG A 702 " --> pdb=" O   HIS A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 711
      removed outlier: 4.055A  pdb=" N   LEU A 709 " --> pdb=" O   ARG A 706 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLU A 710 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   CYS A 711 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 738
    Processing helix  chain 'A' and resid 750 through 761
    Processing helix  chain 'A' and resid 800 through 807
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 823 through 831
      removed outlier: 3.747A  pdb=" N   LEU A 827 " --> pdb=" O   ASP A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 841 through 855
      removed outlier: 3.523A  pdb=" N   GLU A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 868 through 875
      removed outlier: 3.931A  pdb=" N   HIS A 874 " --> pdb=" O   GLY A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 956
    Processing helix  chain 'A' and resid 967 through 1009
      removed outlier: 3.953A  pdb=" N   CYS A 971 " --> pdb=" O   ILE A 967 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A1007 " --> pdb=" O   SER A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1033
      removed outlier: 3.556A  pdb=" N   ARG A1033 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1078
      removed outlier: 3.513A  pdb=" N   ILE A1055 " --> pdb=" O   ASN A1051 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER A1068 " --> pdb=" O   VAL A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1097 through 1118
      removed outlier: 3.648A  pdb=" N   SER A1101 " --> pdb=" O   SER A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1130
    Processing helix  chain 'A' and resid 1131 through 1151
    Processing helix  chain 'A' and resid 1153 through 1160
    Processing helix  chain 'A' and resid 1166 through 1195
      removed outlier: 3.944A  pdb=" N   VAL A1172 " --> pdb=" O   GLU A1168 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.586A  pdb=" N   VAL A 156 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 174
      removed outlier: 3.668A  pdb=" N   PHE A 172 " --> pdb=" O   TYR A 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 313
      removed outlier: 5.248A  pdb=" N   GLN A 302 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A 324 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 322 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 359 through 361
      removed outlier: 3.525A  pdb=" N   GLN A 359 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 347 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS A 361 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   CYS A 345 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN A 392 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASP A 348 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   VAL A 390 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 515
      removed outlier: 6.494A  pdb=" N   GLY A 878 " --> pdb=" O   PHE A 960 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   SER A 962 " --> pdb=" O   GLY A 878 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA A 880 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   THR A 859 " --> pdb=" O   VAL A 877 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   VAL A 879 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   MET A 861 " --> pdb=" O   VAL A 879 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL A 858 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   PHE A 837 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   MET A 745 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LEU A 809 " --> pdb=" O   VAL A 836 " (cutoff:3.500A)
      removed outlier: 8.672A  pdb=" N   ALA A 838 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU A 811 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 770 " --> pdb=" O   ALA A 808 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 772 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   THR A 812 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 544 through 547
      removed outlier: 5.655A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   PHE A 715 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   TYR A 690 " --> pdb=" O   PHE A 715 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY A 717 " --> pdb=" O   LEU A 688 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 687 " --> pdb=" O   GLY A 655 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A 655 " --> pdb=" O   ALA A 687 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 653 " --> pdb=" O   GLY A 689 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 635 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ARG A 632 " --> pdb=" O   PHE A 626 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   PHE A 626 " --> pdb=" O   ARG A 632 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   SER A 638 " --> pdb=" O   ILE A 620 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ILE A 620 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 8.736A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   LEU A 618 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 547
      removed outlier: 5.655A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   PHE A 715 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.910A  pdb=" N   MET A 578 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL A 586 " --> pdb=" O   MET A 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    401 hydrogen bonds defined for protein.
    1146 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: 3.01

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2552
        1.34 -     1.46: 1739
        1.46 -     1.58: 3765
        1.58 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 8125
  Sorted by residual:
  bond pdb=" CG1 ILE A 430 "
       pdb=" CD1 ILE A 430 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.07e+00
  bond pdb=" CB  MET A 229 "
       pdb=" CG  MET A 229 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.68e+00
  bond pdb=" CG  ARG A1079 "
       pdb=" CD  ARG A1079 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.47e-01
  bond pdb=" CB  MET A1110 "
       pdb=" CG  MET A1110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.46e-01
  bond pdb=" CB  THR A 482 "
       pdb=" CG2 THR A 482 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.01e-01
  ... (remaining 8120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 10855
        2.03 -     4.05: 144
        4.05 -     6.08: 22
        6.08 -     8.11: 1
        8.11 -    10.13: 2
  Bond angle restraints: 11024
  Sorted by residual:
  angle pdb=" CB  MET A 229 "
        pdb=" CG  MET A 229 "
        pdb=" SD  MET A 229 "
      ideal   model   delta    sigma   weight residual
     112.70  102.57   10.13 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" CB  MET A 288 "
        pdb=" CG  MET A 288 "
        pdb=" SD  MET A 288 "
      ideal   model   delta    sigma   weight residual
     112.70  121.30   -8.60 3.00e+00 1.11e-01 8.21e+00
  angle pdb=" N   TRP A 257 "
        pdb=" CA  TRP A 257 "
        pdb=" CB  TRP A 257 "
      ideal   model   delta    sigma   weight residual
     110.28  114.63   -4.35 1.55e+00 4.16e-01 7.88e+00
  angle pdb=" CA  TRP A 257 "
        pdb=" CB  TRP A 257 "
        pdb=" CG  TRP A 257 "
      ideal   model   delta    sigma   weight residual
     113.60  118.67   -5.07 1.90e+00 2.77e-01 7.12e+00
  angle pdb=" CA  ARG A 436 "
        pdb=" CB  ARG A 436 "
        pdb=" CG  ARG A 436 "
      ideal   model   delta    sigma   weight residual
     114.10  118.63   -4.53 2.00e+00 2.50e-01 5.14e+00
  ... (remaining 11019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 4506
       17.05 -    34.09: 336
       34.09 -    51.14: 58
       51.14 -    68.19: 4
       68.19 -    85.23: 4
  Dihedral angle restraints: 4908
    sinusoidal: 1946
      harmonic: 2962
  Sorted by residual:
  dihedral pdb=" CA  MET A 229 "
           pdb=" C   MET A 229 "
           pdb=" N   VAL A 230 "
           pdb=" CA  VAL A 230 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.44   27.56     0      5.00e+00 4.00e-02 3.04e+01
  dihedral pdb=" CG  ARG A 520 "
           pdb=" CD  ARG A 520 "
           pdb=" NE  ARG A 520 "
           pdb=" CZ  ARG A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.23  -44.23     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  ASN A 884 "
           pdb=" CB  ASN A 884 "
           pdb=" CG  ASN A 884 "
           pdb=" OD1 ASN A 884 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.75  -66.25     2      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 4905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1063
       0.054 -    0.108: 190
       0.108 -    0.162: 25
       0.162 -    0.217: 1
       0.217 -    0.271: 1
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CG  LEU A 431 "
            pdb=" CB  LEU A 431 "
            pdb=" CD1 LEU A 431 "
            pdb=" CD2 LEU A 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  ILE A 771 "
            pdb=" N   ILE A 771 "
            pdb=" C   ILE A 771 "
            pdb=" CB  ILE A 771 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CB  VAL A 338 "
            pdb=" CA  VAL A 338 "
            pdb=" CG1 VAL A 338 "
            pdb=" CG2 VAL A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.06e-01
  ... (remaining 1277 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 257 "   -0.025 2.00e-02 2.50e+03   2.55e-02 1.63e+01
        pdb=" CG  TRP A 257 "    0.069 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 257 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 257 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 257 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 257 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 257 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 257 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 257 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 257 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 558 "    0.046 5.00e-02 4.00e+02   7.04e-02 7.93e+00
        pdb=" N   PRO A 559 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 559 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 559 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1165 "   -0.034 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO A1166 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A1166 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A1166 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 349
        2.72 -     3.27: 8189
        3.27 -     3.81: 12789
        3.81 -     4.36: 14440
        4.36 -     4.90: 24710
  Nonbonded interactions: 60477
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 558 "
            pdb=" OG  SER A 562 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   LEU A 352 "
            pdb=" ND2 ASN A 867 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG  SER A 328 "
            pdb=" OD1 ASN A 332 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NZ  LYS A 853 "
            pdb=" OD1 ASP A 876 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OE2 GLU A1008 "
            pdb=" NZ  LYS A1083 "
     model   vdw
     2.247 3.120
  ... (remaining 60472 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.640
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
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   0.068   8125  Z= 0.133
  Angle     :  0.578  10.135  11024  Z= 0.297
  Chirality :  0.041   0.271   1280
  Planarity :  0.005   0.070   1398
  Dihedral  : 11.945  85.232   2988
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.27 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.45 (0.26), residues: 1012
  helix:  1.79 (0.24), residues: 441
  sheet:  0.18 (0.57), residues: 97
  loop :  0.47 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.003   TRP A 257 
 HIS   0.004   0.001   HIS A 675 
 PHE   0.029   0.001   PHE A1169 
 TYR   0.017   0.001   TYR A1091 
 ARG   0.012   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16921 (  400)
  hydrogen bonds       : angle       6.07223 ( 1146)
  covalent geometry    : bond        0.00286 ( 8125)
  covalent geometry    : angle       0.57762 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7974 (tpt) cc_final: 0.7625 (tpt)
REVERT: A  276 PHE cc_start: 0.7617 (t80) cc_final: 0.6989 (t80)
REVERT: A  347 VAL cc_start: 0.8607 (p) cc_final: 0.8293 (t)
REVERT: A  351 MET cc_start: 0.6600 (ttt) cc_final: 0.6301 (ttt)
REVERT: A  374 ASP cc_start: 0.7911 (t70) cc_final: 0.7695 (t70)
REVERT: A  476 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7487 (ttpp)
REVERT: A  479 LEU cc_start: 0.8209 (tp) cc_final: 0.7988 (tp)
REVERT: A  492 GLU cc_start: 0.6593 (mp0) cc_final: 0.6186 (mp0)
REVERT: A  626 PHE cc_start: 0.8169 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  631 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7581 (mmpt)
REVERT: A  675 HIS cc_start: 0.8211 (t-90) cc_final: 0.7570 (t-90)
REVERT: A  677 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7267 (mt-10)
REVERT: A  827 LEU cc_start: 0.8578 (tp) cc_final: 0.8340 (tp)
REVERT: A  839 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7039 (ttm-80)
REVERT: A 1027 CYS cc_start: 0.6969 (t) cc_final: 0.6454 (t)
REVERT: A 1065 HIS cc_start: 0.6515 (m-70) cc_final: 0.6302 (m-70)
REVERT: A 1117 ILE cc_start: 0.8592 (tt) cc_final: 0.8366 (tt)
REVERT: A 1132 LYS cc_start: 0.8353 (mttt) cc_final: 0.8046 (mttt)
REVERT: A 1138 LEU cc_start: 0.8330 (mm) cc_final: 0.7965 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2215
  time to fit residues: 70.0160
Evaluate side-chains
  215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0050
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS
A 741 HIS
A1061 GLN
A1118 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.157872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.131984 restraints weight = 13614.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.136442 restraints weight = 6461.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.139404 restraints weight = 3878.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8125  Z= 0.129
  Angle     :  0.595   9.023  11024  Z= 0.300
  Chirality :  0.042   0.178   1280
  Planarity :  0.005   0.055   1398
  Dihedral  :  3.922  20.611   1086
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.57 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.40 (0.26), residues: 1012
  helix:  1.76 (0.24), residues: 443
  sheet:  0.16 (0.60), residues: 87
  loop :  0.41 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.003   TRP A 257 
 HIS   0.007   0.001   HIS A 575 
 PHE   0.025   0.001   PHE A1066 
 TYR   0.015   0.001   TYR A1119 
 ARG   0.006   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04589 (  400)
  hydrogen bonds       : angle       4.62663 ( 1146)
  covalent geometry    : bond        0.00286 ( 8125)
  covalent geometry    : angle       0.59490 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 227
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.5239 (mmm) cc_final: 0.4563 (mmm)
REVERT: A  272 MET cc_start: 0.7884 (tpt) cc_final: 0.7563 (tpt)
REVERT: A  276 PHE cc_start: 0.7601 (t80) cc_final: 0.6986 (t80)
REVERT: A  349 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6839 (mt-10)
REVERT: A  362 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: A  428 ARG cc_start: 0.7786 (tmm160) cc_final: 0.7498 (tmm160)
REVERT: A  479 LEU cc_start: 0.8272 (tp) cc_final: 0.8043 (tp)
REVERT: A  492 GLU cc_start: 0.6655 (mp0) cc_final: 0.6305 (mp0)
REVERT: A  626 PHE cc_start: 0.8200 (m-80) cc_final: 0.7986 (m-10)
REVERT: A  677 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7143 (mt-10)
REVERT: A  726 LYS cc_start: 0.6692 (mtmm) cc_final: 0.6470 (mtmm)
REVERT: A  827 LEU cc_start: 0.8583 (tp) cc_final: 0.8366 (tp)
REVERT: A  845 LYS cc_start: 0.8498 (mttm) cc_final: 0.8023 (mttm)
REVERT: A 1108 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7484 (mmt)
REVERT: A 1117 ILE cc_start: 0.8593 (tt) cc_final: 0.8339 (tt)
REVERT: A 1138 LEU cc_start: 0.8248 (mm) cc_final: 0.7988 (mt)
  outliers start: 10
  outliers final: 4
  residues processed: 228
  average time/residue: 0.2182
  time to fit residues: 65.2208
Evaluate side-chains
  221 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 215
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
A 225 ASN
A 296 ASN
A 359 GLN
A 441 ASN
A 575 HIS
A 741 HIS
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.157019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.130798 restraints weight = 13938.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.135318 restraints weight = 6530.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.138310 restraints weight = 3888.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8125  Z= 0.130
  Angle     :  0.567   8.410  11024  Z= 0.281
  Chirality :  0.041   0.157   1280
  Planarity :  0.005   0.059   1398
  Dihedral  :  3.877  15.788   1086
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.98 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.30 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.33 (0.26), residues: 1012
  helix:  1.76 (0.24), residues: 441
  sheet:  0.02 (0.57), residues: 89
  loop :  0.35 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 257 
 HIS   0.008   0.001   HIS A1065 
 PHE   0.019   0.001   PHE A1066 
 TYR   0.019   0.001   TYR A 671 
 ARG   0.007   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  400)
  hydrogen bonds       : angle       4.32781 ( 1146)
  covalent geometry    : bond        0.00281 ( 8125)
  covalent geometry    : angle       0.56703 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 VAL cc_start: 0.8593 (t) cc_final: 0.8355 (m)
REVERT: A  229 MET cc_start: 0.5287 (mmm) cc_final: 0.4802 (mmm)
REVERT: A  272 MET cc_start: 0.7878 (tpt) cc_final: 0.7573 (tpt)
REVERT: A  276 PHE cc_start: 0.7586 (t80) cc_final: 0.6967 (t80)
REVERT: A  338 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8326 (t)
REVERT: A  362 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7365 (mp0)
REVERT: A  479 LEU cc_start: 0.8292 (tp) cc_final: 0.8047 (tp)
REVERT: A  492 GLU cc_start: 0.6713 (mp0) cc_final: 0.6347 (mp0)
REVERT: A  631 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7762 (mmpt)
REVERT: A  677 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7147 (mt-10)
REVERT: A  827 LEU cc_start: 0.8553 (tp) cc_final: 0.8347 (tp)
REVERT: A  845 LYS cc_start: 0.8478 (mttm) cc_final: 0.8031 (mtpp)
REVERT: A  853 LYS cc_start: 0.7997 (tttp) cc_final: 0.7592 (ttmm)
REVERT: A  963 LYS cc_start: 0.8683 (mttt) cc_final: 0.8318 (mttt)
REVERT: A  987 MET cc_start: 0.7930 (mmm) cc_final: 0.7675 (mtm)
REVERT: A  994 ASN cc_start: 0.7456 (t0) cc_final: 0.7214 (t0)
REVERT: A 1008 GLU cc_start: 0.7892 (tp30) cc_final: 0.7663 (tp30)
REVERT: A 1117 ILE cc_start: 0.8608 (tt) cc_final: 0.8403 (tt)
REVERT: A 1118 ASN cc_start: 0.8147 (m110) cc_final: 0.7706 (m-40)
REVERT: A 1138 LEU cc_start: 0.8235 (mm) cc_final: 0.7960 (mt)
  outliers start: 20
  outliers final: 12
  residues processed: 224
  average time/residue: 0.2260
  time to fit residues: 66.1179
Evaluate side-chains
  228 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 214
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  359 GLN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  441 ASN
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 52 optimal weight:   50.0000
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 HIS
** A1118 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 = 0.4067 r_free = 0.4067 target = 0.155692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.129035 restraints weight = 13792.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133558 restraints weight = 6464.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.136514 restraints weight = 3876.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8125  Z= 0.147
  Angle     :  0.556   7.210  11024  Z= 0.280
  Chirality :  0.042   0.157   1280
  Planarity :  0.005   0.058   1398
  Dihedral  :  3.841  15.110   1086
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.17 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.17 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.29 (0.26), residues: 1012
  helix:  1.72 (0.24), residues: 442
  sheet:  0.04 (0.56), residues: 91
  loop :  0.32 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 257 
 HIS   0.005   0.001   HIS A 299 
 PHE   0.024   0.002   PHE A1066 
 TYR   0.019   0.001   TYR A 671 
 ARG   0.007   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 (  400)
  hydrogen bonds       : angle       4.26912 ( 1146)
  covalent geometry    : bond        0.00321 ( 8125)
  covalent geometry    : angle       0.55647 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 217
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7654 (mtmm)
REVERT: A  196 VAL cc_start: 0.8585 (t) cc_final: 0.8372 (m)
REVERT: A  229 MET cc_start: 0.5419 (mmm) cc_final: 0.5050 (mmm)
REVERT: A  272 MET cc_start: 0.7914 (tpt) cc_final: 0.7599 (tpt)
REVERT: A  276 PHE cc_start: 0.7589 (t80) cc_final: 0.6965 (t80)
REVERT: A  349 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6811 (mt-10)
REVERT: A  362 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7442 (mp0)
REVERT: A  479 LEU cc_start: 0.8307 (tp) cc_final: 0.8043 (tp)
REVERT: A  492 GLU cc_start: 0.6758 (mp0) cc_final: 0.6408 (mp0)
REVERT: A  631 LYS cc_start: 0.8064 (mmpt) cc_final: 0.7784 (mmpt)
REVERT: A  677 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7101 (mt-10)
REVERT: A  734 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7302 (tpp80)
REVERT: A  827 LEU cc_start: 0.8561 (tp) cc_final: 0.8355 (tp)
REVERT: A  845 LYS cc_start: 0.8509 (mttm) cc_final: 0.8110 (mtpp)
REVERT: A  853 LYS cc_start: 0.8079 (tttp) cc_final: 0.7729 (tptm)
REVERT: A  963 LYS cc_start: 0.8652 (mttt) cc_final: 0.8352 (mttt)
REVERT: A  994 ASN cc_start: 0.7501 (t0) cc_final: 0.7262 (t0)
REVERT: A 1008 GLU cc_start: 0.7835 (tp30) cc_final: 0.7617 (tp30)
REVERT: A 1108 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7247 (mmp)
REVERT: A 1118 ASN cc_start: 0.8139 (m110) cc_final: 0.7717 (m-40)
REVERT: A 1138 LEU cc_start: 0.8224 (mm) cc_final: 0.7947 (mt)
  outliers start: 18
  outliers final: 10
  residues processed: 220
  average time/residue: 0.2247
  time to fit residues: 64.4261
Evaluate side-chains
  226 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 214
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 98 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    1.0762

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
A 741 HIS
A1118 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.155140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.129101 restraints weight = 13691.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133531 restraints weight = 6409.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.136414 restraints weight = 3833.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8125  Z= 0.145
  Angle     :  0.570   8.742  11024  Z= 0.281
  Chirality :  0.042   0.151   1280
  Planarity :  0.005   0.058   1398
  Dihedral  :  3.821  14.406   1086
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.47 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.63 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.29 (0.26), residues: 1012
  helix:  1.69 (0.24), residues: 449
  sheet:  0.17 (0.56), residues: 91
  loop :  0.30 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A 257 
 HIS   0.005   0.001   HIS A 299 
 PHE   0.019   0.001   PHE A1066 
 TYR   0.020   0.001   TYR A 671 
 ARG   0.007   0.001   ARG A 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  400)
  hydrogen bonds       : angle       4.20996 ( 1146)
  covalent geometry    : bond        0.00317 ( 8125)
  covalent geometry    : angle       0.57035 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 224
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7650 (mtmm)
REVERT: A  196 VAL cc_start: 0.8584 (t) cc_final: 0.8364 (m)
REVERT: A  229 MET cc_start: 0.5620 (mmm) cc_final: 0.5165 (mmm)
REVERT: A  272 MET cc_start: 0.7909 (tpt) cc_final: 0.7578 (tpt)
REVERT: A  276 PHE cc_start: 0.7609 (t80) cc_final: 0.6975 (t80)
REVERT: A  291 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5018 (mt)
REVERT: A  316 GLU cc_start: 0.6625 (pt0) cc_final: 0.6413 (pt0)
REVERT: A  342 ARG cc_start: 0.6190 (mtp180) cc_final: 0.5978 (mtp180)
REVERT: A  349 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6742 (mt-10)
REVERT: A  360 MET cc_start: 0.6906 (tmm) cc_final: 0.6410 (tmm)
REVERT: A  362 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: A  479 LEU cc_start: 0.8295 (tp) cc_final: 0.8059 (tp)
REVERT: A  492 GLU cc_start: 0.6767 (mp0) cc_final: 0.6446 (mp0)
REVERT: A  631 LYS cc_start: 0.8140 (mmpt) cc_final: 0.7897 (mmpt)
REVERT: A  675 HIS cc_start: 0.8108 (t-90) cc_final: 0.7772 (t-90)
REVERT: A  677 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7017 (mt-10)
REVERT: A  734 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7321 (tpp80)
REVERT: A  773 GLN cc_start: 0.8105 (pm20) cc_final: 0.7606 (pm20)
REVERT: A  785 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6714 (ptp-110)
REVERT: A  845 LYS cc_start: 0.8505 (mttm) cc_final: 0.8080 (mtpp)
REVERT: A  853 LYS cc_start: 0.8125 (tttp) cc_final: 0.7643 (tptm)
REVERT: A  987 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7657 (mtm)
REVERT: A  994 ASN cc_start: 0.7546 (t0) cc_final: 0.7328 (t0)
REVERT: A 1008 GLU cc_start: 0.7826 (tp30) cc_final: 0.7603 (tp30)
REVERT: A 1061 GLN cc_start: 0.7042 (mt0) cc_final: 0.6833 (mt0)
REVERT: A 1110 MET cc_start: 0.7389 (mmp) cc_final: 0.7158 (mmt)
REVERT: A 1118 ASN cc_start: 0.8239 (m-40) cc_final: 0.7884 (m-40)
REVERT: A 1138 LEU cc_start: 0.8220 (mm) cc_final: 0.7975 (mt)
  outliers start: 28
  outliers final: 17
  residues processed: 234
  average time/residue: 0.2252
  time to fit residues: 68.8102
Evaluate side-chains
  241 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 220
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  359 GLN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 741 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.155352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129256 restraints weight = 13704.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.133693 restraints weight = 6407.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.136553 restraints weight = 3835.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8125  Z= 0.130
  Angle     :  0.572   8.584  11024  Z= 0.283
  Chirality :  0.043   0.270   1280
  Planarity :  0.005   0.058   1398
  Dihedral  :  3.801  14.277   1086
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.17 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.11 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.21 (0.26), residues: 1012
  helix:  1.64 (0.24), residues: 450
  sheet: -0.08 (0.53), residues: 98
  loop :  0.28 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 257 
 HIS   0.004   0.001   HIS A 123 
 PHE   0.016   0.001   PHE A1066 
 TYR   0.018   0.001   TYR A 671 
 ARG   0.010   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 (  400)
  hydrogen bonds       : angle       4.18697 ( 1146)
  covalent geometry    : bond        0.00290 ( 8125)
  covalent geometry    : angle       0.57249 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 219
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7659 (mtmm)
REVERT: A  196 VAL cc_start: 0.8551 (t) cc_final: 0.8340 (m)
REVERT: A  225 ASN cc_start: 0.8030 (t0) cc_final: 0.7786 (t0)
REVERT: A  272 MET cc_start: 0.7889 (tpt) cc_final: 0.7663 (tpt)
REVERT: A  276 PHE cc_start: 0.7608 (t80) cc_final: 0.6989 (t80)
REVERT: A  291 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.5021 (mt)
REVERT: A  360 MET cc_start: 0.6900 (tmm) cc_final: 0.6429 (tmm)
REVERT: A  362 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7305 (mp0)
REVERT: A  444 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8376 (t)
REVERT: A  479 LEU cc_start: 0.8298 (tp) cc_final: 0.8016 (tp)
REVERT: A  492 GLU cc_start: 0.6762 (mp0) cc_final: 0.6461 (mp0)
REVERT: A  592 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8061 (mmmm)
REVERT: A  631 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7902 (mmpt)
REVERT: A  675 HIS cc_start: 0.8095 (t-90) cc_final: 0.7782 (t-90)
REVERT: A  677 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6990 (mt-10)
REVERT: A  734 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7331 (tpp80)
REVERT: A  773 GLN cc_start: 0.8146 (pm20) cc_final: 0.7516 (pm20)
REVERT: A  785 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6697 (ptp-110)
REVERT: A  845 LYS cc_start: 0.8511 (mttm) cc_final: 0.8146 (mtpp)
REVERT: A  853 LYS cc_start: 0.8123 (tttp) cc_final: 0.7557 (tptm)
REVERT: A  987 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7638 (mtm)
REVERT: A 1008 GLU cc_start: 0.7792 (tp30) cc_final: 0.7591 (tp30)
REVERT: A 1110 MET cc_start: 0.7444 (mmp) cc_final: 0.7038 (mmp)
REVERT: A 1118 ASN cc_start: 0.8230 (m-40) cc_final: 0.7861 (m-40)
REVERT: A 1138 LEU cc_start: 0.8205 (mm) cc_final: 0.7943 (mt)
  outliers start: 24
  outliers final: 18
  residues processed: 226
  average time/residue: 0.2329
  time to fit residues: 68.4605
Evaluate side-chains
  240 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 217
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1111 GLN
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.0970
   chunk 51 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
A 440 ASN
A 741 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.154851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.128299 restraints weight = 13861.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132823 restraints weight = 6485.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.135772 restraints weight = 3865.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8125  Z= 0.154
  Angle     :  0.588   8.626  11024  Z= 0.290
  Chirality :  0.043   0.224   1280
  Planarity :  0.005   0.058   1398
  Dihedral  :  3.880  14.751   1086
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.37 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.22 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 (0.26), residues: 1012
  helix:  1.54 (0.24), residues: 452
  sheet: -0.13 (0.53), residues: 101
  loop :  0.23 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 257 
 HIS   0.005   0.001   HIS A 123 
 PHE   0.015   0.001   PHE A1066 
 TYR   0.017   0.001   TYR A 671 
 ARG   0.008   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04211 (  400)
  hydrogen bonds       : angle       4.21047 ( 1146)
  covalent geometry    : bond        0.00336 ( 8125)
  covalent geometry    : angle       0.58793 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 223
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7636 (mttp)
REVERT: A  196 VAL cc_start: 0.8578 (t) cc_final: 0.8368 (m)
REVERT: A  272 MET cc_start: 0.7897 (tpt) cc_final: 0.7661 (tpt)
REVERT: A  276 PHE cc_start: 0.7599 (t80) cc_final: 0.6986 (t80)
REVERT: A  291 ILE cc_start: 0.5524 (OUTLIER) cc_final: 0.5140 (mt)
REVERT: A  349 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6911 (mt-10)
REVERT: A  362 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7511 (mp0)
REVERT: A  425 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7456 (mttm)
REVERT: A  444 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8387 (t)
REVERT: A  479 LEU cc_start: 0.8323 (tp) cc_final: 0.8045 (tp)
REVERT: A  485 LEU cc_start: 0.7891 (tt) cc_final: 0.7639 (tp)
REVERT: A  492 GLU cc_start: 0.6759 (mp0) cc_final: 0.6460 (mp0)
REVERT: A  592 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8069 (mmmm)
REVERT: A  631 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7909 (mmpt)
REVERT: A  675 HIS cc_start: 0.8106 (t-90) cc_final: 0.7791 (t-90)
REVERT: A  734 ARG cc_start: 0.7666 (tpp80) cc_final: 0.7339 (tpp80)
REVERT: A  773 GLN cc_start: 0.8157 (pm20) cc_final: 0.7171 (pm20)
REVERT: A  785 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6588 (ptp-110)
REVERT: A  829 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7709 (mtm-85)
REVERT: A  845 LYS cc_start: 0.8547 (mttm) cc_final: 0.8280 (mttm)
REVERT: A  853 LYS cc_start: 0.8142 (tttp) cc_final: 0.7559 (tptm)
REVERT: A  987 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7690 (mtm)
REVERT: A 1049 ILE cc_start: 0.8449 (tp) cc_final: 0.8045 (tt)
REVERT: A 1060 LEU cc_start: 0.7839 (tt) cc_final: 0.7560 (tt)
REVERT: A 1064 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8092 (p)
REVERT: A 1065 HIS cc_start: 0.7181 (m170) cc_final: 0.6603 (m170)
REVERT: A 1106 MET cc_start: 0.7545 (tpt) cc_final: 0.7199 (tpt)
REVERT: A 1110 MET cc_start: 0.7328 (mmp) cc_final: 0.7090 (mmp)
REVERT: A 1118 ASN cc_start: 0.8314 (m-40) cc_final: 0.7972 (m-40)
REVERT: A 1138 LEU cc_start: 0.8217 (mm) cc_final: 0.7986 (mt)
  outliers start: 32
  outliers final: 21
  residues processed: 234
  average time/residue: 0.2311
  time to fit residues: 70.7461
Evaluate side-chains
  250 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 223
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TRP
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  359 GLN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1111 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 55 optimal weight:    0.2980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** 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 = 0.4075 r_free = 0.4075 target = 0.156520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129990 restraints weight = 13817.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.134582 restraints weight = 6516.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.137553 restraints weight = 3880.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8125  Z= 0.124
  Angle     :  0.590   9.717  11024  Z= 0.288
  Chirality :  0.043   0.190   1280
  Planarity :  0.004   0.058   1398
  Dihedral  :  3.844  14.534   1086
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.08 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.79 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 (0.26), residues: 1012
  helix:  1.56 (0.24), residues: 453
  sheet: -0.21 (0.52), residues: 101
  loop :  0.26 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 257 
 HIS   0.005   0.001   HIS A 123 
 PHE   0.015   0.001   PHE A1066 
 TYR   0.017   0.001   TYR A 671 
 ARG   0.007   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  400)
  hydrogen bonds       : angle       4.10435 ( 1146)
  covalent geometry    : bond        0.00279 ( 8125)
  covalent geometry    : angle       0.58960 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 225
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7674 (mtmm)
REVERT: A  196 VAL cc_start: 0.8531 (t) cc_final: 0.8314 (m)
REVERT: A  225 ASN cc_start: 0.8041 (t0) cc_final: 0.7780 (t0)
REVERT: A  257 TRP cc_start: 0.6065 (m-90) cc_final: 0.5818 (m-90)
REVERT: A  272 MET cc_start: 0.7877 (tpt) cc_final: 0.7636 (tpt)
REVERT: A  276 PHE cc_start: 0.7586 (t80) cc_final: 0.7038 (t80)
REVERT: A  291 ILE cc_start: 0.5584 (OUTLIER) cc_final: 0.5210 (mt)
REVERT: A  360 MET cc_start: 0.6848 (tmm) cc_final: 0.6477 (tmm)
REVERT: A  362 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7404 (mp0)
REVERT: A  432 PHE cc_start: 0.6428 (m-10) cc_final: 0.5424 (m-10)
REVERT: A  444 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8377 (t)
REVERT: A  479 LEU cc_start: 0.8317 (tp) cc_final: 0.8044 (tp)
REVERT: A  492 GLU cc_start: 0.6807 (mp0) cc_final: 0.6568 (mp0)
REVERT: A  592 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8033 (mmmm)
REVERT: A  631 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7927 (mmpt)
REVERT: A  675 HIS cc_start: 0.8076 (t-90) cc_final: 0.7794 (t-90)
REVERT: A  726 LYS cc_start: 0.7249 (mptt) cc_final: 0.6996 (mttp)
REVERT: A  734 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7336 (tpp80)
REVERT: A  773 GLN cc_start: 0.8118 (pm20) cc_final: 0.7073 (pm20)
REVERT: A  785 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6590 (ptp-110)
REVERT: A  816 LEU cc_start: 0.8413 (tt) cc_final: 0.8157 (tp)
REVERT: A  846 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7374 (mt-10)
REVERT: A  853 LYS cc_start: 0.8145 (tttp) cc_final: 0.7522 (tptm)
REVERT: A  987 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7637 (mtm)
REVERT: A 1049 ILE cc_start: 0.8427 (tp) cc_final: 0.8038 (tt)
REVERT: A 1060 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7488 (tt)
REVERT: A 1064 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8076 (p)
REVERT: A 1065 HIS cc_start: 0.7168 (m170) cc_final: 0.6868 (m170)
REVERT: A 1110 MET cc_start: 0.7303 (mmp) cc_final: 0.7034 (mmp)
REVERT: A 1118 ASN cc_start: 0.8313 (m-40) cc_final: 0.7901 (m-40)
REVERT: A 1138 LEU cc_start: 0.8197 (mm) cc_final: 0.7948 (mt)
  outliers start: 26
  outliers final: 15
  residues processed: 234
  average time/residue: 0.2159
  time to fit residues: 66.2357
Evaluate side-chains
  241 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 219
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1111 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.155568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.128824 restraints weight = 14009.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.133301 restraints weight = 6601.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.136246 restraints weight = 3970.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8125  Z= 0.129
  Angle     :  0.597   9.371  11024  Z= 0.289
  Chirality :  0.042   0.182   1280
  Planarity :  0.004   0.057   1398
  Dihedral  :  3.839  14.337   1086
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.47 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.93 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 (0.26), residues: 1012
  helix:  1.51 (0.24), residues: 453
  sheet: -0.16 (0.53), residues: 101
  loop :  0.24 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 257 
 HIS   0.006   0.001   HIS A 299 
 PHE   0.014   0.001   PHE A1066 
 TYR   0.016   0.001   TYR A 671 
 ARG   0.010   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  400)
  hydrogen bonds       : angle       4.10588 ( 1146)
  covalent geometry    : bond        0.00291 ( 8125)
  covalent geometry    : angle       0.59723 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7680 (mtmm)
REVERT: A  196 VAL cc_start: 0.8537 (t) cc_final: 0.8310 (m)
REVERT: A  207 ARG cc_start: 0.7700 (mmp80) cc_final: 0.7464 (mmp80)
REVERT: A  225 ASN cc_start: 0.7996 (t0) cc_final: 0.7738 (t0)
REVERT: A  257 TRP cc_start: 0.6229 (m-90) cc_final: 0.5967 (m-90)
REVERT: A  272 MET cc_start: 0.7869 (tpt) cc_final: 0.7626 (tpt)
REVERT: A  276 PHE cc_start: 0.7577 (t80) cc_final: 0.7029 (t80)
REVERT: A  283 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7288 (mm-40)
REVERT: A  349 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6960 (mt-10)
REVERT: A  362 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7527 (mp0)
REVERT: A  392 GLN cc_start: 0.7672 (mt0) cc_final: 0.7469 (tt0)
REVERT: A  425 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7387 (mttm)
REVERT: A  444 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8369 (t)
REVERT: A  479 LEU cc_start: 0.8307 (tp) cc_final: 0.8025 (tp)
REVERT: A  492 GLU cc_start: 0.6782 (mp0) cc_final: 0.6506 (mp0)
REVERT: A  592 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8034 (mmmm)
REVERT: A  631 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7950 (mmpt)
REVERT: A  633 MET cc_start: 0.6791 (tmm) cc_final: 0.6585 (tmm)
REVERT: A  675 HIS cc_start: 0.8064 (t-90) cc_final: 0.7792 (t-90)
REVERT: A  734 ARG cc_start: 0.7642 (tpp80) cc_final: 0.7324 (tpp80)
REVERT: A  773 GLN cc_start: 0.8103 (pm20) cc_final: 0.7086 (pm20)
REVERT: A  785 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6597 (ptp-110)
REVERT: A  829 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7814 (mtm-85)
REVERT: A  853 LYS cc_start: 0.8129 (tttp) cc_final: 0.7473 (tptm)
REVERT: A  987 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7649 (mtm)
REVERT: A  994 ASN cc_start: 0.7458 (t0) cc_final: 0.7218 (t0)
REVERT: A 1046 LEU cc_start: 0.8569 (mm) cc_final: 0.8241 (tp)
REVERT: A 1049 ILE cc_start: 0.8397 (tp) cc_final: 0.8039 (tt)
REVERT: A 1060 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7517 (tp)
REVERT: A 1064 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (p)
REVERT: A 1106 MET cc_start: 0.7529 (tpt) cc_final: 0.7171 (tpt)
REVERT: A 1110 MET cc_start: 0.7383 (mmp) cc_final: 0.7102 (mmt)
REVERT: A 1118 ASN cc_start: 0.8335 (m-40) cc_final: 0.7895 (m-40)
REVERT: A 1138 LEU cc_start: 0.8210 (mm) cc_final: 0.7969 (mt)
  outliers start: 21
  outliers final: 12
  residues processed: 227
  average time/residue: 0.2338
  time to fit residues: 69.8660
Evaluate side-chains
  239 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 221
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 98 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 95 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 GLN
A1065 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.156836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.130274 restraints weight = 13727.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.134758 restraints weight = 6451.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.137716 restraints weight = 3853.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8125  Z= 0.116
  Angle     :  0.590   9.409  11024  Z= 0.285
  Chirality :  0.042   0.171   1280
  Planarity :  0.004   0.058   1398
  Dihedral  :  3.822  17.108   1086
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.70 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  1.07 (0.26), residues: 1012
  helix:  1.53 (0.24), residues: 450
  sheet: -0.31 (0.51), residues: 107
  loop :  0.26 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 257 
 HIS   0.014   0.001   HIS A1065 
 PHE   0.016   0.001   PHE A1066 
 TYR   0.017   0.001   TYR A 671 
 ARG   0.009   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  400)
  hydrogen bonds       : angle       4.05578 ( 1146)
  covalent geometry    : bond        0.00263 ( 8125)
  covalent geometry    : angle       0.58971 (11024)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 222
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 VAL cc_start: 0.8522 (t) cc_final: 0.8284 (m)
REVERT: A  225 ASN cc_start: 0.7981 (t0) cc_final: 0.7718 (t0)
REVERT: A  257 TRP cc_start: 0.6215 (m-90) cc_final: 0.5936 (m-90)
REVERT: A  272 MET cc_start: 0.7869 (tpt) cc_final: 0.7619 (tpt)
REVERT: A  276 PHE cc_start: 0.7621 (t80) cc_final: 0.7008 (t80)
REVERT: A  283 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7283 (mm-40)
REVERT: A  359 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7155 (pm20)
REVERT: A  362 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7545 (mp0)
REVERT: A  444 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8372 (t)
REVERT: A  479 LEU cc_start: 0.8324 (tp) cc_final: 0.8041 (tp)
REVERT: A  492 GLU cc_start: 0.6794 (mp0) cc_final: 0.6579 (mp0)
REVERT: A  631 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7742 (mmtm)
REVERT: A  633 MET cc_start: 0.6772 (tmm) cc_final: 0.6567 (tmm)
REVERT: A  675 HIS cc_start: 0.8075 (t-90) cc_final: 0.7825 (t-90)
REVERT: A  726 LYS cc_start: 0.7297 (mptt) cc_final: 0.7034 (mttp)
REVERT: A  734 ARG cc_start: 0.7645 (tpp80) cc_final: 0.7294 (tpp80)
REVERT: A  773 GLN cc_start: 0.8098 (pm20) cc_final: 0.7058 (pm20)
REVERT: A  785 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6594 (ptp-110)
REVERT: A  829 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7798 (mtm-85)
REVERT: A  853 LYS cc_start: 0.8147 (tttp) cc_final: 0.7655 (tptm)
REVERT: A  854 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6904 (mp0)
REVERT: A  987 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7612 (mtm)
REVERT: A 1049 ILE cc_start: 0.8383 (tp) cc_final: 0.7986 (tt)
REVERT: A 1060 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7489 (tp)
REVERT: A 1064 VAL cc_start: 0.8298 (p) cc_final: 0.8075 (p)
REVERT: A 1106 MET cc_start: 0.7500 (tpt) cc_final: 0.7151 (tpt)
REVERT: A 1118 ASN cc_start: 0.8313 (m-40) cc_final: 0.7904 (m-40)
REVERT: A 1138 LEU cc_start: 0.8207 (mm) cc_final: 0.7954 (mt)
  outliers start: 23
  outliers final: 14
  residues processed: 228
  average time/residue: 0.2187
  time to fit residues: 65.8895
Evaluate side-chains
  239 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  359 GLN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1065 HIS
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0000
   chunk 56 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0970
   overall best weight:    0.4982

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1065 HIS ** 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 = 0.4079 r_free = 0.4079 target = 0.156748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.130207 restraints weight = 13691.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.134686 restraints weight = 6458.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.137622 restraints weight = 3867.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.160   8125  Z= 0.390
  Angle     :  1.204  59.195  11024  Z= 0.732
  Chirality :  0.059   1.447   1280
  Planarity :  0.007   0.206   1398
  Dihedral  :  3.878  20.458   1086
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.27 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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 (0.26), residues: 1012
  helix:  1.54 (0.24), residues: 450
  sheet: -0.29 (0.51), residues: 107
  loop :  0.26 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 257 
 HIS   0.341   0.007   HIS A1065 
 PHE   0.015   0.001   PHE A1066 
 TYR   0.017   0.001   TYR A 671 
 ARG   0.008   0.001   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  400)
  hydrogen bonds       : angle       4.06802 ( 1146)
  covalent geometry    : bond        0.00612 ( 8125)
  covalent geometry    : angle       1.20413 (11024)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2957.57 seconds
wall clock time: 51 minutes 50.36 seconds (3110.36 seconds total)