Starting phenix.real_space_refine
on Thu Jan 18 08:12:49 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd2_17598/01_2024/8pd2_17598.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd2_17598/01_2024/8pd2_17598.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd2_17598/01_2024/8pd2_17598.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd2_17598/01_2024/8pd2_17598.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd2_17598/01_2024/8pd2_17598.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd2_17598/01_2024/8pd2_17598.pdb"
  }
  resolution = 3.25
  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=   0.001 sd=   0.027
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      44      5.16       5
     C    5402      2.51       5
     N    1372      2.21       5
     O    1452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  740": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  999": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1131": "OE1" <-> "OE2"
    Residue "A ASP 1144": "OD1" <-> "OD2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 8270
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1047, 8270
          Classifications: {'peptide': 1047}
          Link IDs: {'PTRANS': 32, 'TRANS': 1014}
          Chain breaks: 4
  Time building chain proxies: 4.61, per 1000 atoms: 0.56
  Number of scatterers: 8270
  At special positions: 0
  Unit cell: (79.42, 120.384, 122.892, 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      44     16.00
     O    1452      8.00
     N    1372      7.00
     C    5402      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  - 3.50
        Amino acid           : False - 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: 3.01
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      77.1% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.761A  pdb=" N   PHE A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 120
      removed outlier: 4.082A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.735A  pdb=" N   HIS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 162 through 188
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.729A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 254
      removed outlier: 4.196A  pdb=" N   THR A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 296 through 318
      removed outlier: 3.548A  pdb=" N   TYR A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 337
    Processing helix  chain 'A' and resid 338 through 341
    Processing helix  chain 'A' and resid 342 through 375
      removed outlier: 3.785A  pdb=" N   THR A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 380
      removed outlier: 3.722A  pdb=" N   VAL A 380 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 411
      removed outlier: 3.710A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 446
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 3.995A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
      removed outlier: 4.959A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 514
    Processing helix  chain 'A' and resid 515 through 519
      removed outlier: 3.554A  pdb=" N   LEU A 518 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA A 519 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 515 through 519'
    Processing helix  chain 'A' and resid 522 through 530
    Processing helix  chain 'A' and resid 571 through 600
    Processing helix  chain 'A' and resid 604 through 621
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 4.572A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   SER A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   TRP A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 3.596A  pdb=" N   TRP A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 665 through 676
      removed outlier: 3.757A  pdb=" N   LEU A 670 " --> pdb=" O   LYS A 666 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   MET A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 691
      removed outlier: 3.816A  pdb=" N   GLU A 681 " --> pdb=" O   HIS A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 706
      removed outlier: 3.873A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 732
    Processing helix  chain 'A' and resid 732 through 755
      removed outlier: 3.597A  pdb=" N   ASN A 736 " --> pdb=" O   LEU A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 3.805A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 783
    Processing helix  chain 'A' and resid 795 through 810
      removed outlier: 3.975A  pdb=" N   MET A 810 " --> pdb=" O   ARG A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 852
      Proline residue:  A 819  - end of helix
      removed outlier: 3.746A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 858
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.792A  pdb=" N   GLN A 877 " --> pdb=" O   THR A 873 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ARG A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
      removed outlier: 3.670A  pdb=" N   ILE A 913 " --> pdb=" O   SER A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 941
      removed outlier: 3.691A  pdb=" N   THR A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 959
      removed outlier: 3.655A  pdb=" N   LEU A 956 " --> pdb=" O   PRO A 952 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 957 " --> pdb=" O   PRO A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 977
    Processing helix  chain 'A' and resid 1043 through 1050
      removed outlier: 3.769A  pdb=" N   LEU A1048 " --> pdb=" O   GLU A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1108
      removed outlier: 3.519A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.374A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.966A  pdb=" N   VAL A 987 " --> pdb=" O   CYS A1059 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   CYS A1059 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   VAL A 989 " --> pdb=" O   VAL A1057 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 6.596A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP A1144 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136

    601 hydrogen bonds defined for protein.
    1773 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.69

  Time building geometry restraints manager: 3.29 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: 2613
        1.34 -     1.46: 1899
        1.46 -     1.58: 3840
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 8433
  Sorted by residual:
  bond pdb=" CA  ILE A 488 "
       pdb=" CB  ILE A 488 "
    ideal  model  delta    sigma   weight residual
    1.534  1.525  0.009 6.80e-03 2.16e+04 1.88e+00
  bond pdb=" CA  PHE A1080 "
       pdb=" CB  PHE A1080 "
    ideal  model  delta    sigma   weight residual
    1.527  1.505  0.022 1.75e-02 3.27e+03 1.59e+00
  bond pdb=" C   HIS A 889 "
       pdb=" N   PRO A 890 "
    ideal  model  delta    sigma   weight residual
    1.335  1.323  0.013 1.30e-02 5.92e+03 9.43e-01
  bond pdb=" CB  MET A1107 "
       pdb=" CG  MET A1107 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.15e-01
  bond pdb=" CA  ILE A 488 "
       pdb=" C   ILE A 488 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.008 8.80e-03 1.29e+04 8.39e-01
  ... (remaining 8428 not shown)

  Histogram of bond angle deviations from ideal:
       98.87 -   105.89: 136
      105.89 -   112.91: 4815
      112.91 -   119.93: 2854
      119.93 -   126.96: 3533
      126.96 -   133.98: 96
  Bond angle restraints: 11434
  Sorted by residual:
  angle pdb=" OG1 THR A 260 "
        pdb=" CB  THR A 260 "
        pdb=" CG2 THR A 260 "
      ideal   model   delta    sigma   weight residual
     109.30  103.33    5.97 2.00e+00 2.50e-01 8.92e+00
  angle pdb=" OG1 THR A 783 "
        pdb=" CB  THR A 783 "
        pdb=" CG2 THR A 783 "
      ideal   model   delta    sigma   weight residual
     109.30  103.37    5.93 2.00e+00 2.50e-01 8.80e+00
  angle pdb=" CA  MET A1107 "
        pdb=" CB  MET A1107 "
        pdb=" CG  MET A1107 "
      ideal   model   delta    sigma   weight residual
     114.10  119.99   -5.89 2.00e+00 2.50e-01 8.67e+00
  angle pdb=" CB  MET A 925 "
        pdb=" CG  MET A 925 "
        pdb=" SD  MET A 925 "
      ideal   model   delta    sigma   weight residual
     112.70  120.65   -7.95 3.00e+00 1.11e-01 7.02e+00
  angle pdb=" CB  MET A 810 "
        pdb=" CG  MET A 810 "
        pdb=" SD  MET A 810 "
      ideal   model   delta    sigma   weight residual
     112.70  120.16   -7.46 3.00e+00 1.11e-01 6.18e+00
  ... (remaining 11429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 4617
       17.18 -    34.35: 344
       34.35 -    51.53: 66
       51.53 -    68.71: 12
       68.71 -    85.88: 7
  Dihedral angle restraints: 5046
    sinusoidal: 1997
      harmonic: 3049
  Sorted by residual:
  dihedral pdb=" CA  ASP A1144 "
           pdb=" CB  ASP A1144 "
           pdb=" CG  ASP A1144 "
           pdb=" OD1 ASP A1144 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.60   54.60     1      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CG  ARG A1185 "
           pdb=" CD  ARG A1185 "
           pdb=" NE  ARG A1185 "
           pdb=" CZ  ARG A1185 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -136.73  -43.27     2      1.50e+01 4.44e-03 1.00e+01
  dihedral pdb=" CA  LEU A 808 "
           pdb=" C   LEU A 808 "
           pdb=" N   ARG A 809 "
           pdb=" CA  ARG A 809 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.51  -15.49     0      5.00e+00 4.00e-02 9.59e+00
  ... (remaining 5043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 947
       0.034 -    0.068: 311
       0.068 -    0.102: 85
       0.102 -    0.136: 25
       0.136 -    0.170: 2
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CB  THR A 260 "
            pdb=" CA  THR A 260 "
            pdb=" OG1 THR A 260 "
            pdb=" CG2 THR A 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CB  THR A 783 "
            pdb=" CA  THR A 783 "
            pdb=" OG1 THR A 783 "
            pdb=" CG2 THR A 783 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CA  ILE A 948 "
            pdb=" N   ILE A 948 "
            pdb=" C   ILE A 948 "
            pdb=" CB  ILE A 948 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 1367 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 209 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO A 210 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 210 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 210 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 275 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO A 276 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 276 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 276 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 818 "    0.023 5.00e-02 4.00e+02   3.55e-02 2.02e+00
        pdb=" N   PRO A 819 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 819 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 819 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2682
        2.84 -     3.35: 8689
        3.35 -     3.87: 13035
        3.87 -     4.38: 14883
        4.38 -     4.90: 25829
  Nonbonded interactions: 65118
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 664 "
            pdb=" CE2 TYR A 665 "
     model   vdw
     2.322 3.420
  nonbonded pdb=" OE1 GLN A 900 "
            pdb=" NH2 ARG A 903 "
     model   vdw
     2.339 2.520
  nonbonded pdb=" N   GLN A1110 "
            pdb=" OE1 GLN A1110 "
     model   vdw
     2.366 2.520
  nonbonded pdb=" N   GLU A 606 "
            pdb=" OE1 GLU A 606 "
     model   vdw
     2.412 2.520
  nonbonded pdb=" OE2 GLU A 581 "
            pdb=" NH1 ARG A 585 "
     model   vdw
     2.419 2.520
  ... (remaining 65113 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          5.920
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     25.460
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
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      :  0.004   0.030   8433  Z= 0.279
  Angle     :  0.520   7.950  11434  Z= 0.286
  Chirality :  0.038   0.170   1370
  Planarity :  0.003   0.039   1407
  Dihedral  : 12.987  85.882   3070
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1037
  helix:  0.83 (0.19), residues: 732
  sheet: -0.58 (0.77), residues: 39
  loop : -0.04 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1112 
 HIS   0.005   0.001   HIS A 914 
 PHE   0.013   0.001   PHE A 365 
 TYR   0.008   0.001   TYR A 309 
 ARG   0.004   0.001   ARG A 809 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 PRO cc_start: 0.7139 (Cg_endo) cc_final: 0.6794 (Cg_exo)
REVERT: A  125 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7326 (mt-10)
REVERT: A  154 MET cc_start: 0.8182 (mtp) cc_final: 0.7935 (mtp)
REVERT: A  155 ASP cc_start: 0.7234 (t0) cc_final: 0.6984 (t0)
REVERT: A  163 PHE cc_start: 0.7505 (t80) cc_final: 0.7142 (t80)
REVERT: A  209 ASP cc_start: 0.7481 (t0) cc_final: 0.6998 (t0)
REVERT: A  233 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7003 (tt0)
REVERT: A  295 ASN cc_start: 0.7472 (t0) cc_final: 0.7226 (t0)
REVERT: A  337 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7236 (mp0)
REVERT: A  346 GLU cc_start: 0.7067 (tt0) cc_final: 0.6829 (tt0)
REVERT: A  375 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7716 (mtpt)
REVERT: A  381 ASP cc_start: 0.7206 (m-30) cc_final: 0.6936 (m-30)
REVERT: A  383 MET cc_start: 0.7419 (mmm) cc_final: 0.6718 (mmm)
REVERT: A  385 TRP cc_start: 0.7899 (m100) cc_final: 0.7652 (m100)
REVERT: A  475 GLN cc_start: 0.8158 (tp40) cc_final: 0.7908 (tp40)
REVERT: A  485 ASP cc_start: 0.7799 (m-30) cc_final: 0.7307 (p0)
REVERT: A  486 ILE cc_start: 0.8089 (mp) cc_final: 0.7758 (mp)
REVERT: A  609 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7120 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6549 (mt-10)
REVERT: A  632 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7679 (mtmm)
REVERT: A  740 PHE cc_start: 0.7072 (t80) cc_final: 0.6246 (t80)
REVERT: A  856 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6590 (ttp80)
REVERT: A  865 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6987 (ttp80)
REVERT: A  911 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6870 (mm-30)
REVERT: A  926 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7063 (mm-30)
REVERT: A  954 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7270 (mp0)
REVERT: A 1003 SER cc_start: 0.8622 (t) cc_final: 0.8121 (p)
REVERT: A 1066 TYR cc_start: 0.8509 (m-80) cc_final: 0.8127 (m-80)
REVERT: A 1116 LYS cc_start: 0.7396 (tppp) cc_final: 0.7165 (tppp)
REVERT: A 1138 ILE cc_start: 0.7408 (mt) cc_final: 0.7142 (mp)
REVERT: A 1173 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6697 (tttt)
REVERT: A 1182 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5601 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7248 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.2442
  time to fit residues: 79.9225
Evaluate side-chains
  214 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 60 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 597 GLN
A 613 GLN
A 685 ASN
A 691 ASN
A 764 ASN
A 831 ASN
A 832 GLN
A 877 GLN
A 886 GLN
A1120 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8433  Z= 0.247
  Angle     :  0.550  10.140  11434  Z= 0.290
  Chirality :  0.041   0.141   1370
  Planarity :  0.004   0.044   1407
  Dihedral  :  3.915  16.696   1119
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.00 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1037
  helix:  1.72 (0.19), residues: 751
  sheet: -0.44 (0.68), residues: 54
  loop :  0.28 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A 676 
 PHE   0.020   0.002   PHE A 769 
 TYR   0.010   0.001   TYR A1066 
 ARG   0.005   0.001   ARG A1185 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 208
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7207 (mt-10)
REVERT: A  154 MET cc_start: 0.8330 (mtp) cc_final: 0.7984 (mtp)
REVERT: A  155 ASP cc_start: 0.7343 (t0) cc_final: 0.7048 (t0)
REVERT: A  163 PHE cc_start: 0.7570 (t80) cc_final: 0.7149 (t80)
REVERT: A  209 ASP cc_start: 0.7510 (t0) cc_final: 0.6994 (t0)
REVERT: A  233 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6928 (tt0)
REVERT: A  250 LYS cc_start: 0.7466 (mttt) cc_final: 0.7149 (mttp)
REVERT: A  337 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7240 (mp0)
REVERT: A  375 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7537 (mtpt)
REVERT: A  381 ASP cc_start: 0.7286 (m-30) cc_final: 0.7036 (m-30)
REVERT: A  383 MET cc_start: 0.7544 (mmm) cc_final: 0.6695 (mmm)
REVERT: A  475 GLN cc_start: 0.8096 (tp40) cc_final: 0.7828 (mm-40)
REVERT: A  485 ASP cc_start: 0.7813 (m-30) cc_final: 0.7286 (p0)
REVERT: A  486 ILE cc_start: 0.8037 (mp) cc_final: 0.7728 (mp)
REVERT: A  584 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7726 (mm)
REVERT: A  609 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.7120 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6320 (mt-10)
REVERT: A  632 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7644 (mtmm)
REVERT: A  646 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6807 (ttp-110)
REVERT: A  671 MET cc_start: 0.7698 (mmp) cc_final: 0.7012 (mmp)
REVERT: A  676 HIS cc_start: 0.7417 (m-70) cc_final: 0.6718 (m-70)
REVERT: A  680 PHE cc_start: 0.7225 (t80) cc_final: 0.7019 (t80)
REVERT: A  740 PHE cc_start: 0.6974 (t80) cc_final: 0.6351 (t80)
REVERT: A  828 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7697 (mmtp)
REVERT: A  832 GLN cc_start: 0.8099 (tp40) cc_final: 0.7871 (tp-100)
REVERT: A  856 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6723 (ttp80)
REVERT: A  900 GLN cc_start: 0.7704 (mm110) cc_final: 0.7267 (mt0)
REVERT: A  926 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6599 (mm-30)
REVERT: A  942 MET cc_start: 0.8336 (mmt) cc_final: 0.7995 (mmt)
REVERT: A  958 LYS cc_start: 0.7772 (ttpp) cc_final: 0.7290 (ttpp)
REVERT: A  993 ASP cc_start: 0.7581 (m-30) cc_final: 0.7204 (m-30)
REVERT: A 1003 SER cc_start: 0.8586 (t) cc_final: 0.8021 (p)
REVERT: A 1066 TYR cc_start: 0.8506 (m-80) cc_final: 0.8102 (m-80)
REVERT: A 1116 LYS cc_start: 0.7439 (tppp) cc_final: 0.7211 (tppp)
REVERT: A 1138 ILE cc_start: 0.7258 (mt) cc_final: 0.7037 (mp)
REVERT: A 1173 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6725 (tttt)
REVERT: A 1190 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.7158 (mmt90)
  outliers start: 19
  outliers final: 10
  residues processed: 215
  average time/residue: 0.2647
  time to fit residues: 73.3925
Evaluate side-chains
  204 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 193
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  938 MET
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1045 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 93 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A1120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8433  Z= 0.243
  Angle     :  0.510  10.538  11434  Z= 0.265
  Chirality :  0.041   0.217   1370
  Planarity :  0.004   0.046   1407
  Dihedral  :  3.779  17.719   1119
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.78 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.26), residues: 1037
  helix:  1.79 (0.19), residues: 761
  sheet: -0.22 (0.72), residues: 54
  loop :  0.07 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 278 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.022   0.001   PHE A 769 
 TYR   0.012   0.001   TYR A 758 
 ARG   0.003   0.000   ARG A 899 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A  125 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7268 (mt-10)
REVERT: A  154 MET cc_start: 0.8395 (mtp) cc_final: 0.8070 (mtp)
REVERT: A  155 ASP cc_start: 0.7413 (t0) cc_final: 0.7208 (t0)
REVERT: A  163 PHE cc_start: 0.7609 (t80) cc_final: 0.7316 (t80)
REVERT: A  209 ASP cc_start: 0.7559 (t0) cc_final: 0.7069 (t0)
REVERT: A  233 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6919 (tt0)
REVERT: A  250 LYS cc_start: 0.7447 (mttt) cc_final: 0.7158 (mttp)
REVERT: A  337 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7268 (mp0)
REVERT: A  375 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7559 (mtpt)
REVERT: A  381 ASP cc_start: 0.7250 (m-30) cc_final: 0.7009 (m-30)
REVERT: A  383 MET cc_start: 0.7530 (mmm) cc_final: 0.6596 (mmm)
REVERT: A  475 GLN cc_start: 0.8003 (tp40) cc_final: 0.7775 (mm-40)
REVERT: A  485 ASP cc_start: 0.7822 (m-30) cc_final: 0.7239 (p0)
REVERT: A  486 ILE cc_start: 0.8060 (mp) cc_final: 0.7831 (mp)
REVERT: A  609 ARG cc_start: 0.7365 (mtp-110) cc_final: 0.7104 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6350 (mt-10)
REVERT: A  632 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7653 (mtmm)
REVERT: A  671 MET cc_start: 0.7629 (mmp) cc_final: 0.6912 (mmp)
REVERT: A  676 HIS cc_start: 0.7365 (m-70) cc_final: 0.6721 (m-70)
REVERT: A  680 PHE cc_start: 0.7236 (t80) cc_final: 0.7006 (t80)
REVERT: A  740 PHE cc_start: 0.6976 (t80) cc_final: 0.6354 (t80)
REVERT: A  809 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7278 (mtm-85)
REVERT: A  828 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7698 (mmtp)
REVERT: A  832 GLN cc_start: 0.7966 (tp40) cc_final: 0.7602 (tp-100)
REVERT: A  856 ARG cc_start: 0.6951 (ttp80) cc_final: 0.6732 (ttp80)
REVERT: A  900 GLN cc_start: 0.7644 (mm110) cc_final: 0.7284 (mt0)
REVERT: A  926 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6617 (mm-30)
REVERT: A  931 GLU cc_start: 0.7251 (tt0) cc_final: 0.6814 (mt-10)
REVERT: A  942 MET cc_start: 0.8301 (mmt) cc_final: 0.7939 (mmt)
REVERT: A  958 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7334 (ttpp)
REVERT: A  967 MET cc_start: 0.6759 (mmm) cc_final: 0.6536 (mmm)
REVERT: A  990 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7257 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7702 (m-30) cc_final: 0.7078 (m-30)
REVERT: A 1003 SER cc_start: 0.8556 (t) cc_final: 0.7882 (m)
REVERT: A 1066 TYR cc_start: 0.8545 (m-80) cc_final: 0.7997 (m-80)
REVERT: A 1116 LYS cc_start: 0.7424 (tppp) cc_final: 0.7213 (tppp)
REVERT: A 1138 ILE cc_start: 0.7196 (mt) cc_final: 0.6981 (mp)
REVERT: A 1173 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6742 (tttt)
REVERT: A 1190 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7032 (mmt90)
  outliers start: 17
  outliers final: 11
  residues processed: 207
  average time/residue: 0.2455
  time to fit residues: 65.8815
Evaluate side-chains
  206 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 195
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   chunk 45 optimal weight:    0.6980
   chunk 63 optimal weight:    7.9990
   chunk 94 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 981 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8433  Z= 0.181
  Angle     :  0.478   9.980  11434  Z= 0.247
  Chirality :  0.039   0.133   1370
  Planarity :  0.004   0.045   1407
  Dihedral  :  3.677  18.227   1119
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.44 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.27), residues: 1037
  helix:  1.93 (0.19), residues: 759
  sheet:  0.09 (0.71), residues: 54
  loop :  0.35 (0.46), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 635 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.021   0.001   PHE A 769 
 TYR   0.008   0.001   TYR A 672 
 ARG   0.005   0.000   ARG A 646 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 196
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 LEU cc_start: 0.7525 (tp) cc_final: 0.7311 (tp)
REVERT: A  125 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7284 (mt-10)
REVERT: A  154 MET cc_start: 0.8303 (mtp) cc_final: 0.7933 (mtp)
REVERT: A  155 ASP cc_start: 0.7418 (t0) cc_final: 0.7188 (t0)
REVERT: A  163 PHE cc_start: 0.7585 (t80) cc_final: 0.7273 (t80)
REVERT: A  187 ASN cc_start: 0.7558 (m-40) cc_final: 0.7146 (m-40)
REVERT: A  209 ASP cc_start: 0.7522 (t0) cc_final: 0.7022 (t0)
REVERT: A  233 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6971 (tt0)
REVERT: A  250 LYS cc_start: 0.7436 (mttt) cc_final: 0.7172 (mttp)
REVERT: A  320 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7689 (mt-10)
REVERT: A  337 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7263 (mp0)
REVERT: A  346 GLU cc_start: 0.7036 (tt0) cc_final: 0.6668 (tt0)
REVERT: A  367 MET cc_start: 0.7521 (mtp) cc_final: 0.7287 (mtp)
REVERT: A  375 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7578 (mtpt)
REVERT: A  381 ASP cc_start: 0.7189 (m-30) cc_final: 0.6948 (m-30)
REVERT: A  383 MET cc_start: 0.7494 (mmm) cc_final: 0.6635 (mmm)
REVERT: A  475 GLN cc_start: 0.7997 (tp40) cc_final: 0.7768 (mm-40)
REVERT: A  485 ASP cc_start: 0.7857 (m-30) cc_final: 0.7238 (p0)
REVERT: A  486 ILE cc_start: 0.8056 (mp) cc_final: 0.7828 (mp)
REVERT: A  609 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7100 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6367 (mt-10)
REVERT: A  632 LYS cc_start: 0.7892 (mtmt) cc_final: 0.7606 (mtmm)
REVERT: A  671 MET cc_start: 0.7643 (mmp) cc_final: 0.6873 (mmp)
REVERT: A  676 HIS cc_start: 0.7323 (m-70) cc_final: 0.6710 (m-70)
REVERT: A  680 PHE cc_start: 0.7160 (t80) cc_final: 0.6953 (t80)
REVERT: A  740 PHE cc_start: 0.7012 (t80) cc_final: 0.6411 (t80)
REVERT: A  828 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7663 (mmtp)
REVERT: A  832 GLN cc_start: 0.7967 (tp40) cc_final: 0.7591 (tp-100)
REVERT: A  856 ARG cc_start: 0.6964 (ttp80) cc_final: 0.6759 (ttp80)
REVERT: A  931 GLU cc_start: 0.7187 (tt0) cc_final: 0.6931 (mt-10)
REVERT: A  942 MET cc_start: 0.8254 (mmt) cc_final: 0.7870 (mmt)
REVERT: A  958 LYS cc_start: 0.7812 (ttpp) cc_final: 0.7318 (ttpp)
REVERT: A  967 MET cc_start: 0.6800 (mmm) cc_final: 0.6436 (mmm)
REVERT: A  990 ARG cc_start: 0.7876 (ptp-110) cc_final: 0.7306 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7741 (m-30) cc_final: 0.7144 (m-30)
REVERT: A 1003 SER cc_start: 0.8573 (t) cc_final: 0.7883 (m)
REVERT: A 1104 MET cc_start: 0.7470 (mmm) cc_final: 0.7251 (tpp)
REVERT: A 1123 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7773 (mtm110)
REVERT: A 1173 LYS cc_start: 0.7218 (ttpt) cc_final: 0.6731 (tttt)
REVERT: A 1190 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6850 (mmt90)
  outliers start: 15
  outliers final: 11
  residues processed: 205
  average time/residue: 0.2584
  time to fit residues: 68.2484
Evaluate side-chains
  204 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 193
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
A 757 HIS
A 981 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8433  Z= 0.399
  Angle     :  0.549   9.293  11434  Z= 0.283
  Chirality :  0.043   0.141   1370
  Planarity :  0.004   0.048   1407
  Dihedral  :  3.807  18.787   1119
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.78 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.26), residues: 1037
  helix:  1.61 (0.18), residues: 762
  sheet:  0.06 (0.67), residues: 54
  loop :  0.13 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 278 
 HIS   0.005   0.001   HIS A 676 
 PHE   0.024   0.002   PHE A 769 
 TYR   0.013   0.001   TYR A 758 
 ARG   0.003   0.000   ARG A 646 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 206
  time to evaluate  : 1.341 
Fit side-chains
REVERT: A  121 PRO cc_start: 0.6614 (Cg_endo) cc_final: 0.6150 (Cg_exo)
REVERT: A  122 LEU cc_start: 0.7496 (tp) cc_final: 0.7208 (tp)
REVERT: A  125 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7255 (mt-10)
REVERT: A  154 MET cc_start: 0.8312 (mtp) cc_final: 0.7904 (mtp)
REVERT: A  155 ASP cc_start: 0.7373 (t0) cc_final: 0.7122 (t0)
REVERT: A  163 PHE cc_start: 0.7686 (t80) cc_final: 0.7354 (t80)
REVERT: A  209 ASP cc_start: 0.7623 (t0) cc_final: 0.7162 (t0)
REVERT: A  233 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6913 (tt0)
REVERT: A  250 LYS cc_start: 0.7418 (mttt) cc_final: 0.7180 (mttp)
REVERT: A  320 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7780 (mt-10)
REVERT: A  337 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7268 (mp0)
REVERT: A  344 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6844 (mt-10)
REVERT: A  346 GLU cc_start: 0.7100 (tt0) cc_final: 0.6754 (tt0)
REVERT: A  375 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7548 (mtpt)
REVERT: A  381 ASP cc_start: 0.7364 (m-30) cc_final: 0.7137 (m-30)
REVERT: A  383 MET cc_start: 0.7469 (mmm) cc_final: 0.6798 (mmm)
REVERT: A  475 GLN cc_start: 0.7996 (tp40) cc_final: 0.7760 (mm-40)
REVERT: A  485 ASP cc_start: 0.7824 (m-30) cc_final: 0.7147 (p0)
REVERT: A  486 ILE cc_start: 0.8038 (mp) cc_final: 0.7783 (mp)
REVERT: A  609 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.7164 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6531 (mt-10)
REVERT: A  632 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7657 (mtmm)
REVERT: A  671 MET cc_start: 0.7609 (mmp) cc_final: 0.6813 (mmp)
REVERT: A  676 HIS cc_start: 0.7414 (m-70) cc_final: 0.6750 (m-70)
REVERT: A  680 PHE cc_start: 0.7213 (t80) cc_final: 0.6991 (t80)
REVERT: A  828 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7789 (mmtp)
REVERT: A  856 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6744 (ttp80)
REVERT: A  926 GLU cc_start: 0.7073 (mp0) cc_final: 0.6631 (mm-30)
REVERT: A  958 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7357 (ttpp)
REVERT: A  990 ARG cc_start: 0.7862 (ptp-110) cc_final: 0.7229 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7767 (m-30) cc_final: 0.7129 (m-30)
REVERT: A 1003 SER cc_start: 0.8563 (t) cc_final: 0.7864 (m)
REVERT: A 1066 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7891 (m-80)
REVERT: A 1104 MET cc_start: 0.7560 (mmm) cc_final: 0.7320 (tpp)
REVERT: A 1110 GLN cc_start: 0.7405 (mp10) cc_final: 0.7203 (mp10)
REVERT: A 1173 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6764 (tttt)
REVERT: A 1190 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.6988 (mmt90)
  outliers start: 21
  outliers final: 12
  residues processed: 218
  average time/residue: 0.2742
  time to fit residues: 77.9222
Evaluate side-chains
  215 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1069 THR
Chi-restraints excluded: chain A residue 1116 LYS
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0870
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 832 GLN
A 981 HIS
A1191 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8433  Z= 0.202
  Angle     :  0.479   8.782  11434  Z= 0.248
  Chirality :  0.039   0.157   1370
  Planarity :  0.004   0.046   1407
  Dihedral  :  3.697  19.670   1119
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.22 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.26), residues: 1037
  helix:  1.91 (0.19), residues: 758
  sheet:  0.38 (0.68), residues: 52
  loop :  0.27 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 635 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.023   0.001   PHE A 769 
 TYR   0.017   0.001   TYR A 758 
 ARG   0.004   0.000   ARG A 899 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.7509 (tp) cc_final: 0.7294 (tp)
REVERT: A  125 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7291 (mt-10)
REVERT: A  154 MET cc_start: 0.8279 (mtp) cc_final: 0.7941 (mtp)
REVERT: A  155 ASP cc_start: 0.7357 (t0) cc_final: 0.7100 (t0)
REVERT: A  163 PHE cc_start: 0.7624 (t80) cc_final: 0.7306 (t80)
REVERT: A  187 ASN cc_start: 0.7566 (m-40) cc_final: 0.7139 (m-40)
REVERT: A  209 ASP cc_start: 0.7549 (t0) cc_final: 0.7079 (t0)
REVERT: A  233 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6916 (tt0)
REVERT: A  250 LYS cc_start: 0.7422 (mttt) cc_final: 0.7170 (mttp)
REVERT: A  337 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7240 (mp0)
REVERT: A  346 GLU cc_start: 0.7045 (tt0) cc_final: 0.6690 (tt0)
REVERT: A  375 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7660 (mtpt)
REVERT: A  381 ASP cc_start: 0.7340 (m-30) cc_final: 0.7116 (m-30)
REVERT: A  383 MET cc_start: 0.7404 (mmm) cc_final: 0.6752 (mmm)
REVERT: A  475 GLN cc_start: 0.7979 (tp40) cc_final: 0.7732 (mm-40)
REVERT: A  485 ASP cc_start: 0.7834 (m-30) cc_final: 0.7139 (p0)
REVERT: A  486 ILE cc_start: 0.8031 (mp) cc_final: 0.7585 (mm)
REVERT: A  609 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.7133 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6501 (mt-10)
REVERT: A  632 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7432 (mtmm)
REVERT: A  671 MET cc_start: 0.7600 (mmp) cc_final: 0.6812 (mmp)
REVERT: A  676 HIS cc_start: 0.7374 (m-70) cc_final: 0.6706 (m-70)
REVERT: A  740 PHE cc_start: 0.6960 (t80) cc_final: 0.6400 (t80)
REVERT: A  828 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7702 (mmtp)
REVERT: A  900 GLN cc_start: 0.7699 (mm110) cc_final: 0.7380 (mt0)
REVERT: A  926 GLU cc_start: 0.7033 (mp0) cc_final: 0.6475 (mm-30)
REVERT: A  958 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7323 (ttpp)
REVERT: A  967 MET cc_start: 0.6853 (mmm) cc_final: 0.6417 (mmm)
REVERT: A  990 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.7304 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7830 (m-30) cc_final: 0.7290 (m-30)
REVERT: A 1003 SER cc_start: 0.8549 (t) cc_final: 0.7865 (m)
REVERT: A 1072 ASP cc_start: 0.6992 (m-30) cc_final: 0.6664 (t0)
REVERT: A 1104 MET cc_start: 0.7584 (mmm) cc_final: 0.7319 (tpp)
REVERT: A 1173 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6706 (tttt)
REVERT: A 1190 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6925 (mmt90)
  outliers start: 16
  outliers final: 15
  residues processed: 206
  average time/residue: 0.2376
  time to fit residues: 64.4171
Evaluate side-chains
  208 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 193
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1069 THR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   chunk 84 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0970
   chunk 40 optimal weight:    0.4980
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 165 GLN
A 832 GLN
A 981 HIS
A1191 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8433  Z= 0.177
  Angle     :  0.462   7.454  11434  Z= 0.241
  Chirality :  0.038   0.167   1370
  Planarity :  0.004   0.046   1407
  Dihedral  :  3.590  19.382   1119
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.22 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.26), residues: 1037
  helix:  2.06 (0.19), residues: 758
  sheet:  0.50 (0.68), residues: 52
  loop :  0.33 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 635 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.020   0.001   PHE A 769 
 TYR   0.019   0.001   TYR A 758 
 ARG   0.011   0.000   ARG A 856 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 204
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 PRO cc_start: 0.6541 (Cg_endo) cc_final: 0.6063 (Cg_exo)
REVERT: A  122 LEU cc_start: 0.7534 (tp) cc_final: 0.7279 (tp)
REVERT: A  125 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7294 (mt-10)
REVERT: A  154 MET cc_start: 0.8200 (mtp) cc_final: 0.7948 (mtp)
REVERT: A  155 ASP cc_start: 0.7380 (t0) cc_final: 0.7065 (t0)
REVERT: A  163 PHE cc_start: 0.7602 (t80) cc_final: 0.7280 (t80)
REVERT: A  187 ASN cc_start: 0.7563 (m-40) cc_final: 0.7131 (m-40)
REVERT: A  205 MET cc_start: 0.7748 (tpp) cc_final: 0.6768 (mmt)
REVERT: A  233 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6919 (tt0)
REVERT: A  337 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7234 (mp0)
REVERT: A  346 GLU cc_start: 0.7014 (tt0) cc_final: 0.6652 (tt0)
REVERT: A  367 MET cc_start: 0.7532 (mtp) cc_final: 0.7268 (mtp)
REVERT: A  375 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7653 (mtpt)
REVERT: A  381 ASP cc_start: 0.7367 (m-30) cc_final: 0.7136 (m-30)
REVERT: A  383 MET cc_start: 0.7393 (mmm) cc_final: 0.6729 (mmm)
REVERT: A  475 GLN cc_start: 0.7965 (tp40) cc_final: 0.7707 (mm-40)
REVERT: A  485 ASP cc_start: 0.7831 (m-30) cc_final: 0.7124 (p0)
REVERT: A  486 ILE cc_start: 0.8004 (mp) cc_final: 0.7575 (mm)
REVERT: A  579 MET cc_start: 0.7036 (tpt) cc_final: 0.6594 (tpt)
REVERT: A  609 ARG cc_start: 0.7365 (mtp-110) cc_final: 0.7125 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6489 (mt-10)
REVERT: A  632 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7419 (mtmm)
REVERT: A  671 MET cc_start: 0.7580 (mmp) cc_final: 0.6795 (mmp)
REVERT: A  676 HIS cc_start: 0.7337 (m-70) cc_final: 0.6648 (m-70)
REVERT: A  740 PHE cc_start: 0.6982 (t80) cc_final: 0.6370 (t80)
REVERT: A  758 TYR cc_start: 0.7359 (t80) cc_final: 0.6814 (t80)
REVERT: A  828 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7701 (mmtp)
REVERT: A  832 GLN cc_start: 0.7973 (tp40) cc_final: 0.7657 (tp-100)
REVERT: A  862 LYS cc_start: 0.7602 (ttmm) cc_final: 0.7271 (ttmm)
REVERT: A  877 GLN cc_start: 0.8307 (tt0) cc_final: 0.8059 (tt0)
REVERT: A  926 GLU cc_start: 0.7057 (mp0) cc_final: 0.6629 (mm-30)
REVERT: A  958 LYS cc_start: 0.7803 (ttpp) cc_final: 0.7296 (ttpp)
REVERT: A  967 MET cc_start: 0.6891 (mmm) cc_final: 0.6435 (mmm)
REVERT: A  990 ARG cc_start: 0.7909 (ptp-110) cc_final: 0.7313 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7849 (m-30) cc_final: 0.7312 (m-30)
REVERT: A 1003 SER cc_start: 0.8544 (t) cc_final: 0.7807 (m)
REVERT: A 1051 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8437 (mttp)
REVERT: A 1066 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7906 (m-80)
REVERT: A 1104 MET cc_start: 0.7555 (mmm) cc_final: 0.7299 (tpp)
REVERT: A 1173 LYS cc_start: 0.7263 (ttpt) cc_final: 0.6725 (tttt)
  outliers start: 23
  outliers final: 17
  residues processed: 216
  average time/residue: 0.2231
  time to fit residues: 63.7473
Evaluate side-chains
  216 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1069 THR
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 981 HIS
A1149 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8433  Z= 0.250
  Angle     :  0.489   7.621  11434  Z= 0.253
  Chirality :  0.039   0.168   1370
  Planarity :  0.004   0.048   1407
  Dihedral  :  3.650  19.409   1119
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.11 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.26), residues: 1037
  helix:  1.98 (0.19), residues: 758
  sheet:  0.48 (0.68), residues: 52
  loop :  0.24 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.020   0.001   PHE A 769 
 TYR   0.017   0.001   TYR A 758 
 ARG   0.007   0.000   ARG A 856 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 PRO cc_start: 0.6567 (Cg_endo) cc_final: 0.6100 (Cg_exo)
REVERT: A  122 LEU cc_start: 0.7514 (tp) cc_final: 0.7253 (tp)
REVERT: A  125 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7303 (mt-10)
REVERT: A  154 MET cc_start: 0.8279 (mtp) cc_final: 0.7973 (mtp)
REVERT: A  155 ASP cc_start: 0.7487 (t0) cc_final: 0.7222 (t0)
REVERT: A  163 PHE cc_start: 0.7607 (t80) cc_final: 0.7285 (t80)
REVERT: A  187 ASN cc_start: 0.7571 (m-40) cc_final: 0.7145 (m-40)
REVERT: A  205 MET cc_start: 0.7813 (tpp) cc_final: 0.7546 (mmt)
REVERT: A  209 ASP cc_start: 0.7556 (t0) cc_final: 0.7082 (t0)
REVERT: A  233 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6928 (tt0)
REVERT: A  320 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7712 (mm-30)
REVERT: A  337 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7235 (mp0)
REVERT: A  346 GLU cc_start: 0.7045 (tt0) cc_final: 0.6693 (tt0)
REVERT: A  375 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7635 (mtpt)
REVERT: A  381 ASP cc_start: 0.7400 (m-30) cc_final: 0.7165 (m-30)
REVERT: A  383 MET cc_start: 0.7381 (mmm) cc_final: 0.6725 (mmm)
REVERT: A  475 GLN cc_start: 0.7959 (tp40) cc_final: 0.7702 (mm-40)
REVERT: A  485 ASP cc_start: 0.7839 (m-30) cc_final: 0.7109 (p0)
REVERT: A  486 ILE cc_start: 0.8022 (mp) cc_final: 0.7580 (mm)
REVERT: A  579 MET cc_start: 0.7030 (tpt) cc_final: 0.6693 (tpt)
REVERT: A  609 ARG cc_start: 0.7383 (mtp-110) cc_final: 0.7149 (mtm-85)
REVERT: A  621 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6534 (mt-10)
REVERT: A  632 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7427 (mtmm)
REVERT: A  671 MET cc_start: 0.7569 (mmp) cc_final: 0.6778 (mmp)
REVERT: A  676 HIS cc_start: 0.7349 (m-70) cc_final: 0.6648 (m-70)
REVERT: A  740 PHE cc_start: 0.7026 (t80) cc_final: 0.6448 (t80)
REVERT: A  828 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7703 (mmtp)
REVERT: A  926 GLU cc_start: 0.7119 (mp0) cc_final: 0.6725 (mm-30)
REVERT: A  958 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7301 (ttpp)
REVERT: A  967 MET cc_start: 0.6913 (mmm) cc_final: 0.6441 (mmm)
REVERT: A  990 ARG cc_start: 0.7924 (ptp-110) cc_final: 0.7296 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7839 (m-30) cc_final: 0.7292 (m-30)
REVERT: A 1003 SER cc_start: 0.8498 (t) cc_final: 0.7779 (m)
REVERT: A 1051 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8448 (mttp)
REVERT: A 1066 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7914 (m-80)
REVERT: A 1072 ASP cc_start: 0.6972 (m-30) cc_final: 0.6680 (t0)
REVERT: A 1104 MET cc_start: 0.7599 (mmm) cc_final: 0.7337 (tpp)
REVERT: A 1173 LYS cc_start: 0.7262 (ttpt) cc_final: 0.6718 (tttt)
  outliers start: 24
  outliers final: 16
  residues processed: 212
  average time/residue: 0.2184
  time to fit residues: 61.4822
Evaluate side-chains
  215 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1069 THR
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0030
   chunk 40 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 981 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8433  Z= 0.205
  Angle     :  0.472   7.985  11434  Z= 0.245
  Chirality :  0.039   0.156   1370
  Planarity :  0.004   0.047   1407
  Dihedral  :  3.599  19.193   1119
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.56 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.26), residues: 1037
  helix:  2.06 (0.19), residues: 758
  sheet:  0.57 (0.68), residues: 52
  loop :  0.29 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 635 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.019   0.001   PHE A 769 
 TYR   0.026   0.001   TYR A 758 
 ARG   0.007   0.000   ARG A 856 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 PRO cc_start: 0.6552 (Cg_endo) cc_final: 0.6093 (Cg_exo)
REVERT: A  122 LEU cc_start: 0.7512 (tp) cc_final: 0.7259 (tp)
REVERT: A  125 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7294 (mt-10)
REVERT: A  154 MET cc_start: 0.8315 (mtp) cc_final: 0.7998 (mtp)
REVERT: A  155 ASP cc_start: 0.7445 (t0) cc_final: 0.7186 (t0)
REVERT: A  163 PHE cc_start: 0.7595 (t80) cc_final: 0.7256 (t80)
REVERT: A  187 ASN cc_start: 0.7575 (m-40) cc_final: 0.7148 (m-40)
REVERT: A  205 MET cc_start: 0.7754 (tpp) cc_final: 0.6789 (mmt)
REVERT: A  209 ASP cc_start: 0.7542 (t0) cc_final: 0.7068 (t0)
REVERT: A  233 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6935 (tt0)
REVERT: A  337 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7233 (mp0)
REVERT: A  346 GLU cc_start: 0.7029 (tt0) cc_final: 0.6670 (tt0)
REVERT: A  375 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7637 (mtpt)
REVERT: A  381 ASP cc_start: 0.7403 (m-30) cc_final: 0.7163 (m-30)
REVERT: A  383 MET cc_start: 0.7370 (mmm) cc_final: 0.6759 (mtp)
REVERT: A  475 GLN cc_start: 0.7947 (tp40) cc_final: 0.7687 (mm-40)
REVERT: A  485 ASP cc_start: 0.7839 (m-30) cc_final: 0.7101 (p0)
REVERT: A  486 ILE cc_start: 0.8018 (mp) cc_final: 0.7583 (mm)
REVERT: A  579 MET cc_start: 0.7022 (tpt) cc_final: 0.6685 (tpt)
REVERT: A  609 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.7144 (mtm-85)
REVERT: A  632 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7408 (mtmm)
REVERT: A  671 MET cc_start: 0.7555 (mmp) cc_final: 0.6854 (mmt)
REVERT: A  676 HIS cc_start: 0.7353 (m-70) cc_final: 0.6638 (m-70)
REVERT: A  740 PHE cc_start: 0.7027 (t80) cc_final: 0.6466 (t80)
REVERT: A  828 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7697 (mmtp)
REVERT: A  862 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7298 (ttmm)
REVERT: A  926 GLU cc_start: 0.7125 (mp0) cc_final: 0.6686 (mm-30)
REVERT: A  958 LYS cc_start: 0.7807 (ttpp) cc_final: 0.7279 (ttpp)
REVERT: A  967 MET cc_start: 0.6946 (mmm) cc_final: 0.6476 (mmm)
REVERT: A  990 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7371 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7862 (m-30) cc_final: 0.7436 (m-30)
REVERT: A 1003 SER cc_start: 0.8476 (t) cc_final: 0.8116 (t)
REVERT: A 1051 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8456 (mttp)
REVERT: A 1066 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7936 (m-80)
REVERT: A 1072 ASP cc_start: 0.6934 (m-30) cc_final: 0.6647 (t0)
REVERT: A 1104 MET cc_start: 0.7595 (mmm) cc_final: 0.7325 (tpp)
REVERT: A 1173 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6712 (tttt)
  outliers start: 21
  outliers final: 18
  residues processed: 211
  average time/residue: 0.2301
  time to fit residues: 64.6375
Evaluate side-chains
  217 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1069 THR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.1980
   chunk 68 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0570
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 65 optimal weight:    7.9990
   chunk 87 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 981 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8433  Z= 0.172
  Angle     :  0.476   9.308  11434  Z= 0.243
  Chirality :  0.038   0.147   1370
  Planarity :  0.004   0.047   1407
  Dihedral  :  3.556  18.990   1119
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.78 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.26), residues: 1037
  helix:  2.15 (0.19), residues: 757
  sheet:  0.64 (0.68), residues: 52
  loop :  0.34 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.018   0.001   PHE A 769 
 TYR   0.023   0.001   TYR A 758 
 ARG   0.006   0.000   ARG A 856 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 202
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 PRO cc_start: 0.6500 (Cg_endo) cc_final: 0.6040 (Cg_exo)
REVERT: A  122 LEU cc_start: 0.7516 (tp) cc_final: 0.7268 (tp)
REVERT: A  125 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7292 (mt-10)
REVERT: A  154 MET cc_start: 0.8264 (mtp) cc_final: 0.8028 (mtp)
REVERT: A  155 ASP cc_start: 0.7439 (t0) cc_final: 0.7180 (t0)
REVERT: A  163 PHE cc_start: 0.7510 (t80) cc_final: 0.7217 (t80)
REVERT: A  187 ASN cc_start: 0.7581 (m-40) cc_final: 0.7165 (m-40)
REVERT: A  205 MET cc_start: 0.7720 (tpp) cc_final: 0.6720 (mmt)
REVERT: A  209 ASP cc_start: 0.7517 (t0) cc_final: 0.7024 (t0)
REVERT: A  233 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6910 (tt0)
REVERT: A  320 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7534 (mm-30)
REVERT: A  337 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7236 (mp0)
REVERT: A  346 GLU cc_start: 0.7006 (tt0) cc_final: 0.6645 (tt0)
REVERT: A  375 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7625 (mtpt)
REVERT: A  381 ASP cc_start: 0.7404 (m-30) cc_final: 0.7158 (m-30)
REVERT: A  383 MET cc_start: 0.7368 (mmm) cc_final: 0.6788 (mtp)
REVERT: A  475 GLN cc_start: 0.7945 (tp40) cc_final: 0.7675 (mm-40)
REVERT: A  485 ASP cc_start: 0.7838 (m-30) cc_final: 0.7094 (p0)
REVERT: A  486 ILE cc_start: 0.8013 (mp) cc_final: 0.7572 (mm)
REVERT: A  609 ARG cc_start: 0.7366 (mtp-110) cc_final: 0.7138 (mtm-85)
REVERT: A  632 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7387 (mtmm)
REVERT: A  671 MET cc_start: 0.7531 (mmp) cc_final: 0.6826 (mmt)
REVERT: A  676 HIS cc_start: 0.7344 (m-70) cc_final: 0.6631 (m-70)
REVERT: A  740 PHE cc_start: 0.6971 (t80) cc_final: 0.6413 (t80)
REVERT: A  828 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7691 (mmtp)
REVERT: A  862 LYS cc_start: 0.7591 (ttmm) cc_final: 0.7263 (ttmm)
REVERT: A  958 LYS cc_start: 0.7808 (ttpp) cc_final: 0.7293 (ttpp)
REVERT: A  967 MET cc_start: 0.6957 (mmm) cc_final: 0.6474 (mmm)
REVERT: A  990 ARG cc_start: 0.7935 (ptp-110) cc_final: 0.7379 (ptp-110)
REVERT: A  993 ASP cc_start: 0.7857 (m-30) cc_final: 0.7428 (m-30)
REVERT: A 1003 SER cc_start: 0.8420 (t) cc_final: 0.8050 (t)
REVERT: A 1033 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7724 (mt-10)
REVERT: A 1051 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8459 (mttp)
REVERT: A 1066 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7942 (m-80)
REVERT: A 1072 ASP cc_start: 0.6919 (m-30) cc_final: 0.6649 (t0)
REVERT: A 1104 MET cc_start: 0.7581 (mmm) cc_final: 0.7305 (tpp)
REVERT: A 1173 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6708 (tttt)
  outliers start: 20
  outliers final: 17
  residues processed: 212
  average time/residue: 0.2268
  time to fit residues: 63.6245
Evaluate side-chains
  216 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1069 THR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0020
   chunk 82 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0570
   overall best weight:    0.4506

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 165 GLN
A 981 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.133275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.112826 restraints weight = 11219.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.67
r_work: 0.3222 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8433  Z= 0.167
  Angle     :  0.469   8.911  11434  Z= 0.241
  Chirality :  0.038   0.144   1370
  Planarity :  0.004   0.047   1407
  Dihedral  :  3.513  18.812   1119
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.44 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.26), residues: 1037
  helix:  2.19 (0.19), residues: 758
  sheet:  0.70 (0.69), residues: 52
  loop :  0.43 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.018   0.001   PHE A 769 
 TYR   0.023   0.001   TYR A 758 
 ARG   0.006   0.000   ARG A 856 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2242.84 seconds
wall clock time: 41 minutes 3.89 seconds (2463.89 seconds total)