Starting phenix.real_space_refine
on Sat Apr  6 11:28:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/04_2024/8pd9_17607_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/04_2024/8pd9_17607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/04_2024/8pd9_17607.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/04_2024/8pd9_17607.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/04_2024/8pd9_17607_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/04_2024/8pd9_17607_updated.pdb"
  }
  resolution = 3.6
  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=   0.020
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      41      5.16       5
     C    5289      2.51       5
     N    1346      2.21       5
     O    1430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   92": "NH1" <-> "NH2"
    Residue "A ARG  128": "NH1" <-> "NH2"
    Residue "A ARG  161": "NH1" <-> "NH2"
    Residue "A ARG  351": "NH1" <-> "NH2"
    Residue "A ARG  399": "NH1" <-> "NH2"
    Residue "A ARG  412": "NH1" <-> "NH2"
    Residue "A ARG  420": "NH1" <-> "NH2"
    Residue "A ARG  431": "NH1" <-> "NH2"
    Residue "A ARG  479": "NH1" <-> "NH2"
    Residue "A ARG  491": "NH1" <-> "NH2"
    Residue "A ARG  499": "NH1" <-> "NH2"
    Residue "A ARG  500": "NH1" <-> "NH2"
    Residue "A ARG  507": "NH1" <-> "NH2"
    Residue "A ARG  516": "NH1" <-> "NH2"
    Residue "A ARG  573": "NH1" <-> "NH2"
    Residue "A ARG  583": "NH1" <-> "NH2"
    Residue "A ARG  585": "NH1" <-> "NH2"
    Residue "A ARG  605": "NH1" <-> "NH2"
    Residue "A ARG  609": "NH1" <-> "NH2"
    Residue "A ARG  646": "NH1" <-> "NH2"
    Residue "A ARG  733": "NH1" <-> "NH2"
    Residue "A ARG  756": "NH1" <-> "NH2"
    Residue "A ARG  803": "NH1" <-> "NH2"
    Residue "A ARG  806": "NH1" <-> "NH2"
    Residue "A ARG  809": "NH1" <-> "NH2"
    Residue "A ARG  812": "NH1" <-> "NH2"
    Residue "A ARG  856": "NH1" <-> "NH2"
    Residue "A ARG  865": "NH1" <-> "NH2"
    Residue "A ARG  875": "NH1" <-> "NH2"
    Residue "A ARG  887": "NH1" <-> "NH2"
    Residue "A ARG  899": "NH1" <-> "NH2"
    Residue "A ARG  903": "NH1" <-> "NH2"
    Residue "A ARG  910": "NH1" <-> "NH2"
    Residue "A ARG  940": "NH1" <-> "NH2"
    Residue "A ARG  976": "NH1" <-> "NH2"
    Residue "A ARG 1053": "NH1" <-> "NH2"
    Residue "A ARG 1092": "NH1" <-> "NH2"
    Residue "A ARG 1097": "NH1" <-> "NH2"
    Residue "A ARG 1123": "NH1" <-> "NH2"
    Residue "A ARG 1158": "NH1" <-> "NH2"
    Residue "A ARG 1162": "NH1" <-> "NH2"
    Residue "A ARG 1169": "NH1" <-> "NH2"
    Residue "A ARG 1185": "NH1" <-> "NH2"
    Residue "A ARG 1190": "NH1" <-> "NH2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 8107
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1024, 8085
          Classifications: {'peptide': 1024}
          Link IDs: {'PTRANS': 30, 'TRANS': 993}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 4.74, per 1000 atoms: 0.58
  Number of scatterers: 8107
  At special positions: 0
  Unit cell: (81.76, 115.486, 125.706, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P       1     15.00
     O    1430      8.00
     N    1346      7.00
     C    5289      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: 3.03
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      70.2% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 94
      removed outlier: 3.957A  pdb=" N   ILE A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 119
      removed outlier: 3.544A  pdb=" N   ASN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 4.012A  pdb=" N   HIS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 138
      No H-bonds generated for 'chain 'A' and resid 135 through 138'
    Processing helix  chain 'A' and resid 142 through 152
    Processing helix  chain 'A' and resid 156 through 161
    Processing helix  chain 'A' and resid 163 through 188
    Processing helix  chain 'A' and resid 195 through 205
    Processing helix  chain 'A' and resid 210 through 219
      removed outlier: 3.797A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A 215 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 253
      removed outlier: 3.603A  pdb=" N   LYS A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 292
      removed outlier: 3.588A  pdb=" N   ALA A 274 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
      removed outlier: 3.645A  pdb=" N   HIS A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 316
      removed outlier: 3.607A  pdb=" N   THR A 308 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 336
    Processing helix  chain 'A' and resid 338 through 340
      No H-bonds generated for 'chain 'A' and resid 338 through 340'
    Processing helix  chain 'A' and resid 343 through 375
    Processing helix  chain 'A' and resid 377 through 379
      No H-bonds generated for 'chain 'A' and resid 377 through 379'
    Processing helix  chain 'A' and resid 382 through 412
      removed outlier: 3.697A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
      removed outlier: 4.101A  pdb=" N   ARG A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
      removed outlier: 3.598A  pdb=" N   VAL A 423 " --> pdb=" O   TRP A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 446
    Processing helix  chain 'A' and resid 450 through 468
    Processing helix  chain 'A' and resid 470 through 480
      removed outlier: 5.127A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 514
      removed outlier: 3.516A  pdb=" N   LYS A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 514 " --> pdb=" O   ASN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 530
    Processing helix  chain 'A' and resid 572 through 599
      removed outlier: 3.688A  pdb=" N   ASP A 577 " --> pdb=" O   ARG A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 620
      removed outlier: 3.902A  pdb=" N   ASP A 620 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 635
      removed outlier: 4.096A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   SER A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   TRP A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 3.613A  pdb=" N   ASP A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 651 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 705
      removed outlier: 4.117A  pdb=" N   ILE A 684 " --> pdb=" O   PHE A 680 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 3.797A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL A 700 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASP A 703 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   LYS A 704 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 754
      removed outlier: 4.005A  pdb=" N   ILE A 734 " --> pdb=" O   ASP A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 3.670A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 782
    Processing helix  chain 'A' and resid 799 through 802
      No H-bonds generated for 'chain 'A' and resid 799 through 802'
    Processing helix  chain 'A' and resid 804 through 857
      removed outlier: 4.035A  pdb=" N   MET A 810 " --> pdb=" O   ARG A 806 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 811 " --> pdb=" O   GLY A 807 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   LEU A 813 " --> pdb=" O   ARG A 809 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   THR A 814 " --> pdb=" O   MET A 810 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LYS A 815 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   ALA A 816 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU A 817 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
      Proline residue:  A 819  - end of helix
      removed outlier: 3.572A  pdb=" N   LEU A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ARG A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 888
      removed outlier: 3.515A  pdb=" N   LEU A 885 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ARG A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 919
    Processing helix  chain 'A' and resid 926 through 943
      removed outlier: 3.588A  pdb=" N   LEU A 941 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   MET A 942 " --> pdb=" O   MET A 938 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ASN A 943 " --> pdb=" O   LYS A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 959
    Processing helix  chain 'A' and resid 967 through 974
    Processing helix  chain 'A' and resid 1044 through 1048
      removed outlier: 3.980A  pdb=" N   LEU A1048 " --> pdb=" O   GLU A1044 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1044 through 1048'
    Processing helix  chain 'A' and resid 1070 through 1079
    Processing helix  chain 'A' and resid 1086 through 1107
      removed outlier: 3.657A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1114 through 1123
      removed outlier: 3.709A  pdb=" N   ARG A1123 " --> pdb=" O   LEU A1119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1180 through 1182
      No H-bonds generated for 'chain 'A' and resid 1180 through 1182'
    Processing sheet with id=  A, first strand: chain 'A' and resid 978 through 981
      removed outlier: 6.289A  pdb=" N   TYR A1066 " --> pdb=" O   ILE A1001 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   ILE A1001 " --> pdb=" O   TYR A1066 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ILE A1068 " --> pdb=" O   PHE A 999 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   PHE A 999 " --> pdb=" O   ILE A1068 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 1032 through 1036
    Processing sheet with id=  C, first strand: chain 'A' and resid 1134 through 1136
    Processing sheet with id=  D, first strand: chain 'A' and resid 1142 through 1147
      removed outlier: 6.844A  pdb=" N   VAL A1189 " --> pdb=" O   GLU A1143 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   VAL A1145 " --> pdb=" O   PHE A1187 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   PHE A1187 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)

    500 hydrogen bonds defined for protein.
    1467 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: 2.51

  Time building geometry restraints manager: 3.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2536
        1.34 -     1.46: 1089
        1.46 -     1.58: 4564
        1.58 -     1.70: 2
        1.70 -     1.81: 76
  Bond restraints: 8267
  Sorted by residual:
  bond pdb=" C4  CMP A1401 "
       pdb=" C5  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.349  0.141 2.00e-02 2.50e+03 4.97e+01
  bond pdb=" C5  CMP A1401 "
       pdb=" C6  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.389  0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" C8  CMP A1401 "
       pdb=" N9  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.337  1.400 -0.063 2.00e-02 2.50e+03 9.83e+00
  bond pdb=" C1' CMP A1401 "
       pdb=" O4' CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.412  1.456 -0.044 1.50e-02 4.44e+03 8.50e+00
  bond pdb=" O2P CMP A1401 "
       pdb=" P   CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.510  1.565 -0.055 2.00e-02 2.50e+03 7.47e+00
  ... (remaining 8262 not shown)

  Histogram of bond angle deviations from ideal:
       99.83 -   106.79: 214
      106.79 -   113.75: 4815
      113.75 -   120.72: 3624
      120.72 -   127.68: 2479
      127.68 -   134.64: 86
  Bond angle restraints: 11218
  Sorted by residual:
  angle pdb=" N   TYR A 743 "
        pdb=" CA  TYR A 743 "
        pdb=" C   TYR A 743 "
      ideal   model   delta    sigma   weight residual
     110.97  105.77    5.20 1.09e+00 8.42e-01 2.27e+01
  angle pdb=" OD1 ASN A1040 "
        pdb=" CG  ASN A1040 "
        pdb=" ND2 ASN A1040 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+01
  angle pdb=" N   GLY A1010 "
        pdb=" CA  GLY A1010 "
        pdb=" C   GLY A1010 "
      ideal   model   delta    sigma   weight residual
     110.38  116.39   -6.01 1.48e+00 4.57e-01 1.65e+01
  angle pdb=" N   ALA A 964 "
        pdb=" CA  ALA A 964 "
        pdb=" C   ALA A 964 "
      ideal   model   delta    sigma   weight residual
     111.71  116.14   -4.43 1.15e+00 7.56e-01 1.49e+01
  angle pdb=" C   ILE A 742 "
        pdb=" N   TYR A 743 "
        pdb=" CA  TYR A 743 "
      ideal   model   delta    sigma   weight residual
     120.65  115.99    4.66 1.32e+00 5.74e-01 1.24e+01
  ... (remaining 11213 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.32: 4746
       25.32 -    50.64: 168
       50.64 -    75.96: 13
       75.96 -   101.28: 2
      101.28 -   126.61: 3
  Dihedral angle restraints: 4932
    sinusoidal: 1953
      harmonic: 2979
  Sorted by residual:
  dihedral pdb=" C3' CMP A1401 "
           pdb=" O3' CMP A1401 "
           pdb=" P   CMP A1401 "
           pdb=" O1P CMP A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  173.39  126.61     1      2.00e+01 2.50e-03 3.83e+01
  dihedral pdb=" C5' CMP A1401 "
           pdb=" O5' CMP A1401 "
           pdb=" P   CMP A1401 "
           pdb=" O1P CMP A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00 -173.83 -126.17     1      2.00e+01 2.50e-03 3.82e+01
  dihedral pdb=" CA  LEU A 963 "
           pdb=" C   LEU A 963 "
           pdb=" N   ALA A 964 "
           pdb=" CA  ALA A 964 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.15  -21.85     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 4929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1062
       0.048 -    0.097: 225
       0.097 -    0.145: 50
       0.145 -    0.194: 9
       0.194 -    0.242: 2
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" CA  THR A1049 "
            pdb=" N   THR A1049 "
            pdb=" C   THR A1049 "
            pdb=" CB  THR A1049 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ARG A1097 "
            pdb=" N   ARG A1097 "
            pdb=" C   ARG A1097 "
            pdb=" CB  ARG A1097 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  LYS A1050 "
            pdb=" N   LYS A1050 "
            pdb=" C   LYS A1050 "
            pdb=" CB  LYS A1050 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.82e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1009 "    0.069 2.00e-02 2.50e+03   3.48e-02 2.42e+01
        pdb=" CG  TYR A1009 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1009 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1009 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1009 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1009 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1009 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A1009 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' CMP A1401 "    0.049 2.00e-02 2.50e+03   2.51e-02 1.73e+01
        pdb=" C2  CMP A1401 "   -0.027 2.00e-02 2.50e+03
        pdb=" C4  CMP A1401 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5  CMP A1401 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6  CMP A1401 "    0.003 2.00e-02 2.50e+03
        pdb=" C8  CMP A1401 "   -0.038 2.00e-02 2.50e+03
        pdb=" N1  CMP A1401 "    0.001 2.00e-02 2.50e+03
        pdb=" N3  CMP A1401 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6  CMP A1401 "    0.044 2.00e-02 2.50e+03
        pdb=" N7  CMP A1401 "   -0.015 2.00e-02 2.50e+03
        pdb=" N9  CMP A1401 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 962 "    0.033 2.00e-02 2.50e+03   2.39e-02 1.43e+01
        pdb=" CG  TRP A 962 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 962 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 962 "   -0.042 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 962 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 962 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 962 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 962 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 962 "    0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 962 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 721
        2.74 -     3.28: 8736
        3.28 -     3.82: 13325
        3.82 -     4.36: 14780
        4.36 -     4.90: 25834
  Nonbonded interactions: 63396
  Sorted by model distance:
  nonbonded pdb=" O   ILE A  81 "
            pdb=" OG  SER A  84 "
     model   vdw
     2.197 2.440
  nonbonded pdb=" OH  TYR A 743 "
            pdb=" OD2 ASP A 767 "
     model   vdw
     2.268 2.440
  nonbonded pdb=" OE2 GLU A 746 "
            pdb=" CD  LYS A 750 "
     model   vdw
     2.327 3.440
  nonbonded pdb=" O   ASP A1078 "
            pdb=" OD1 ASP A1078 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   ASP A 650 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.372 2.440
  ... (remaining 63391 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:          5.780
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     25.170
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
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      :  0.005   0.141   8267  Z= 0.300
  Angle     :  0.735   7.271  11218  Z= 0.450
  Chirality :  0.043   0.242   1348
  Planarity :  0.005   0.079   1378
  Dihedral  : 13.444 126.606   3000
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  7.84 %
    Favored  : 92.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 1012
  helix:  1.91 (0.19), residues: 712
  sheet: -0.90 (0.63), residues: 61
  loop :  0.37 (0.44), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 962 
 HIS   0.002   0.000   HIS A 928 
 PHE   0.018   0.002   PHE A1032 
 TYR   0.069   0.002   TYR A1009 
 ARG   0.006   0.000   ARG A1053 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 309
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.6780 (mm) cc_final: 0.6556 (mt)
REVERT: A  134 ASP cc_start: 0.7521 (m-30) cc_final: 0.6518 (p0)
REVERT: A  149 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6673 (tm-30)
REVERT: A  155 ASP cc_start: 0.6515 (t0) cc_final: 0.6081 (t0)
REVERT: A  157 HIS cc_start: 0.6930 (m90) cc_final: 0.6287 (m-70)
REVERT: A  160 MET cc_start: 0.7443 (mmt) cc_final: 0.6873 (mmt)
REVERT: A  163 PHE cc_start: 0.7509 (t80) cc_final: 0.7250 (t80)
REVERT: A  209 ASP cc_start: 0.7282 (t0) cc_final: 0.6839 (t0)
REVERT: A  220 LEU cc_start: 0.7081 (mm) cc_final: 0.6809 (mt)
REVERT: A  288 PHE cc_start: 0.7585 (t80) cc_final: 0.7038 (t80)
REVERT: A  289 PHE cc_start: 0.7463 (m-80) cc_final: 0.7234 (m-10)
REVERT: A  483 MET cc_start: 0.7348 (mtp) cc_final: 0.7109 (mtm)
REVERT: A  485 ASP cc_start: 0.7754 (m-30) cc_final: 0.7395 (p0)
REVERT: A  486 ILE cc_start: 0.7593 (mt) cc_final: 0.7276 (tp)
REVERT: A  500 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7196 (tpp80)
REVERT: A  517 PHE cc_start: 0.6182 (m-80) cc_final: 0.5848 (m-80)
REVERT: A  579 MET cc_start: 0.7017 (tmm) cc_final: 0.6714 (tmm)
REVERT: A  580 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7568 (mm-30)
REVERT: A  583 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6800 (ttp80)
REVERT: A  591 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7521 (mttt)
REVERT: A  606 GLU cc_start: 0.7031 (tp30) cc_final: 0.6538 (tp30)
REVERT: A  609 ARG cc_start: 0.7824 (tpp80) cc_final: 0.6690 (tpp80)
REVERT: A  613 GLN cc_start: 0.8122 (tt0) cc_final: 0.7559 (mt0)
REVERT: A  616 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6686 (mt-10)
REVERT: A  621 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6029 (mt-10)
REVERT: A  632 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7523 (mttt)
REVERT: A  810 MET cc_start: 0.6128 (mpp) cc_final: 0.5425 (mpp)
REVERT: A  828 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6955 (tppt)
REVERT: A  859 ASP cc_start: 0.7459 (m-30) cc_final: 0.7176 (t0)
REVERT: A  863 ILE cc_start: 0.6277 (mm) cc_final: 0.6042 (mm)
REVERT: A  867 LEU cc_start: 0.6398 (mp) cc_final: 0.6078 (mt)
REVERT: A  870 ILE cc_start: 0.6404 (mt) cc_final: 0.6084 (mm)
REVERT: A  876 LEU cc_start: 0.6779 (mp) cc_final: 0.6568 (mm)
REVERT: A  880 LYS cc_start: 0.7402 (tttt) cc_final: 0.7056 (ttpt)
REVERT: A  887 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6969 (mtp85)
REVERT: A  915 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7009 (mt-10)
REVERT: A  926 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6769 (tt0)
REVERT: A  938 MET cc_start: 0.7635 (tpp) cc_final: 0.7285 (ttt)
REVERT: A  940 ARG cc_start: 0.7090 (mtt-85) cc_final: 0.6863 (mtm-85)
REVERT: A  954 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7116 (mt-10)
REVERT: A  966 ASP cc_start: 0.7310 (t0) cc_final: 0.6857 (p0)
REVERT: A  967 MET cc_start: 0.7773 (mtm) cc_final: 0.7338 (mtm)
REVERT: A  969 LEU cc_start: 0.8429 (tp) cc_final: 0.7889 (tp)
REVERT: A  993 ASP cc_start: 0.6845 (m-30) cc_final: 0.6495 (t70)
REVERT: A  994 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7590 (mt-10)
REVERT: A  998 LEU cc_start: 0.6575 (mp) cc_final: 0.6345 (mp)
REVERT: A  999 PHE cc_start: 0.7263 (m-80) cc_final: 0.7019 (m-80)
REVERT: A 1033 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6429 (mt-10)
REVERT: A 1035 TYR cc_start: 0.7867 (m-80) cc_final: 0.7454 (m-80)
REVERT: A 1037 THR cc_start: 0.7432 (t) cc_final: 0.7070 (t)
REVERT: A 1040 ASN cc_start: 0.7447 (m110) cc_final: 0.7100 (m110)
REVERT: A 1042 ILE cc_start: 0.6463 (mt) cc_final: 0.6186 (tt)
REVERT: A 1045 MET cc_start: 0.6961 (mtp) cc_final: 0.6721 (mtp)
REVERT: A 1050 LYS cc_start: 0.7830 (mttt) cc_final: 0.7613 (mmmt)
REVERT: A 1051 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7737 (ttmm)
REVERT: A 1059 CYS cc_start: 0.6908 (m) cc_final: 0.6495 (m)
REVERT: A 1061 THR cc_start: 0.7606 (p) cc_final: 0.7166 (p)
REVERT: A 1071 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: A 1073 MET cc_start: 0.7923 (mmm) cc_final: 0.7547 (mmp)
REVERT: A 1085 SER cc_start: 0.8246 (t) cc_final: 0.7872 (m)
REVERT: A 1098 ILE cc_start: 0.7594 (tp) cc_final: 0.7322 (tt)
REVERT: A 1122 GLU cc_start: 0.7721 (tp30) cc_final: 0.7521 (mm-30)
REVERT: A 1168 SER cc_start: 0.7593 (t) cc_final: 0.7248 (p)
REVERT: A 1183 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7077 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2406
  time to fit residues: 95.9997
Evaluate side-chains
  264 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0040
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0670
   chunk 41 optimal weight:    0.0070
   chunk 79 optimal weight:    0.0270
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.1606

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 889 HIS
A 900 GLN
A1054 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8267  Z= 0.157
  Angle     :  0.535   8.575  11218  Z= 0.273
  Chirality :  0.039   0.130   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.318 147.201   1104
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.00 %
    Favored  : 83.07 %
  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:  2.67 (0.27), residues: 1012
  helix:  2.37 (0.20), residues: 697
  sheet: -0.31 (0.66), residues: 61
  loop :  0.70 (0.44), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 962 
 HIS   0.002   0.000   HIS A 762 
 PHE   0.019   0.001   PHE A 739 
 TYR   0.018   0.001   TYR A 984 
 ARG   0.011   0.001   ARG A 856 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 262
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.5989 (mptt) cc_final: 0.5736 (mppt)
REVERT: A  134 ASP cc_start: 0.7638 (m-30) cc_final: 0.6677 (p0)
REVERT: A  149 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6630 (tm-30)
REVERT: A  155 ASP cc_start: 0.6376 (t0) cc_final: 0.5577 (p0)
REVERT: A  157 HIS cc_start: 0.6855 (m90) cc_final: 0.6059 (m-70)
REVERT: A  160 MET cc_start: 0.7404 (mmt) cc_final: 0.6862 (mmt)
REVERT: A  174 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5817 (tp)
REVERT: A  209 ASP cc_start: 0.7213 (t0) cc_final: 0.6675 (t0)
REVERT: A  238 ASP cc_start: 0.5956 (m-30) cc_final: 0.5716 (m-30)
REVERT: A  337 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7338 (mp0)
REVERT: A  443 GLU cc_start: 0.7254 (tm-30) cc_final: 0.7026 (tm-30)
REVERT: A  475 GLN cc_start: 0.7601 (tp40) cc_final: 0.7262 (tp-100)
REVERT: A  485 ASP cc_start: 0.7787 (m-30) cc_final: 0.7411 (p0)
REVERT: A  486 ILE cc_start: 0.7639 (mt) cc_final: 0.7407 (tp)
REVERT: A  500 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7065 (ttm-80)
REVERT: A  579 MET cc_start: 0.6954 (tmm) cc_final: 0.6688 (tmm)
REVERT: A  580 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7618 (mm-30)
REVERT: A  583 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7049 (ttp80)
REVERT: A  585 ARG cc_start: 0.7042 (mtt-85) cc_final: 0.6729 (tpp80)
REVERT: A  588 LYS cc_start: 0.7549 (ttpp) cc_final: 0.7141 (ttpp)
REVERT: A  591 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7623 (mttt)
REVERT: A  595 TRP cc_start: 0.7385 (m100) cc_final: 0.7156 (m100)
REVERT: A  599 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7048 (mt-10)
REVERT: A  606 GLU cc_start: 0.6953 (tp30) cc_final: 0.6249 (tp30)
REVERT: A  616 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6940 (mt-10)
REVERT: A  630 ASP cc_start: 0.7946 (m-30) cc_final: 0.7660 (m-30)
REVERT: A  705 MET cc_start: 0.2697 (mmt) cc_final: 0.2349 (mmm)
REVERT: A  810 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5725 (mpp)
REVERT: A  828 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6886 (tppt)
REVERT: A  856 ARG cc_start: 0.6891 (ptp90) cc_final: 0.6017 (ptp90)
REVERT: A  857 MET cc_start: 0.7327 (tpp) cc_final: 0.7028 (tpp)
REVERT: A  859 ASP cc_start: 0.7681 (m-30) cc_final: 0.7351 (t0)
REVERT: A  863 ILE cc_start: 0.6155 (mm) cc_final: 0.5944 (mm)
REVERT: A  872 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6483 (mm-30)
REVERT: A  880 LYS cc_start: 0.7410 (tttt) cc_final: 0.7075 (ttpp)
REVERT: A  887 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6832 (mtp85)
REVERT: A  915 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6982 (mt-10)
REVERT: A  926 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6747 (tt0)
REVERT: A  938 MET cc_start: 0.7639 (tpp) cc_final: 0.7325 (ttm)
REVERT: A  940 ARG cc_start: 0.7129 (mtt-85) cc_final: 0.6884 (mtm-85)
REVERT: A  946 SER cc_start: 0.8049 (p) cc_final: 0.7394 (t)
REVERT: A  954 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7036 (mt-10)
REVERT: A  966 ASP cc_start: 0.7366 (t0) cc_final: 0.6929 (t0)
REVERT: A  968 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7655 (mtmt)
REVERT: A  993 ASP cc_start: 0.6923 (m-30) cc_final: 0.6708 (m-30)
REVERT: A 1033 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6252 (mt-10)
REVERT: A 1035 TYR cc_start: 0.7988 (m-80) cc_final: 0.7785 (m-80)
REVERT: A 1050 LYS cc_start: 0.7495 (mttt) cc_final: 0.7262 (mmmt)
REVERT: A 1061 THR cc_start: 0.7648 (p) cc_final: 0.6954 (p)
REVERT: A 1071 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7972 (mt-10)
REVERT: A 1073 MET cc_start: 0.7815 (mmm) cc_final: 0.7489 (mmp)
REVERT: A 1085 SER cc_start: 0.8166 (t) cc_final: 0.7912 (m)
REVERT: A 1122 GLU cc_start: 0.7664 (tp30) cc_final: 0.7379 (mm-30)
REVERT: A 1142 LEU cc_start: 0.7130 (tp) cc_final: 0.6900 (mt)
REVERT: A 1143 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6814 (mm-30)
REVERT: A 1168 SER cc_start: 0.7561 (t) cc_final: 0.7169 (p)
REVERT: A 1183 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6978 (mm-30)
REVERT: A 1185 ARG cc_start: 0.6314 (mmm160) cc_final: 0.6017 (mmm-85)
REVERT: A 1190 ARG cc_start: 0.7106 (mmt180) cc_final: 0.6636 (mmm160)
  outliers start: 17
  outliers final: 10
  residues processed: 269
  average time/residue: 0.2455
  time to fit residues: 85.3796
Evaluate side-chains
  262 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 250
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1129 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 900 GLN
A1120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8267  Z= 0.244
  Angle     :  0.527   8.892  11218  Z= 0.274
  Chirality :  0.040   0.180   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.248 145.331   1104
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.57 %
    Favored  : 81.36 %
  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:  2.28 (0.27), residues: 1012
  helix:  2.08 (0.20), residues: 706
  sheet: -0.33 (0.70), residues: 61
  loop :  0.43 (0.43), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 962 
 HIS   0.003   0.001   HIS A 869 
 PHE   0.023   0.001   PHE A 739 
 TYR   0.009   0.001   TYR A 312 
 ARG   0.008   0.001   ARG A 976 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 241
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.6642 (mmt) cc_final: 0.5875 (mmt)
REVERT: A  134 ASP cc_start: 0.7620 (m-30) cc_final: 0.6567 (p0)
REVERT: A  149 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6626 (tm-30)
REVERT: A  155 ASP cc_start: 0.6362 (t0) cc_final: 0.5632 (p0)
REVERT: A  157 HIS cc_start: 0.6898 (m90) cc_final: 0.6533 (m90)
REVERT: A  160 MET cc_start: 0.7487 (mmt) cc_final: 0.6938 (mmt)
REVERT: A  168 ILE cc_start: 0.6726 (tt) cc_final: 0.6386 (pt)
REVERT: A  199 MET cc_start: 0.7539 (mmm) cc_final: 0.7120 (mmm)
REVERT: A  209 ASP cc_start: 0.7380 (t0) cc_final: 0.6798 (t0)
REVERT: A  238 ASP cc_start: 0.6038 (m-30) cc_final: 0.5739 (m-30)
REVERT: A  373 THR cc_start: 0.6915 (m) cc_final: 0.6621 (m)
REVERT: A  383 MET cc_start: 0.7390 (mmm) cc_final: 0.7080 (tpp)
REVERT: A  443 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6992 (tm-30)
REVERT: A  475 GLN cc_start: 0.7541 (tp40) cc_final: 0.7011 (tp-100)
REVERT: A  485 ASP cc_start: 0.7787 (m-30) cc_final: 0.7401 (p0)
REVERT: A  486 ILE cc_start: 0.7700 (mt) cc_final: 0.7460 (tp)
REVERT: A  500 ARG cc_start: 0.7531 (tpp80) cc_final: 0.7229 (tpp80)
REVERT: A  511 MET cc_start: 0.7847 (tmm) cc_final: 0.7646 (tmm)
REVERT: A  585 ARG cc_start: 0.7186 (mtt-85) cc_final: 0.6941 (ttm170)
REVERT: A  588 LYS cc_start: 0.7607 (ttpp) cc_final: 0.7163 (ttpp)
REVERT: A  599 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7186 (mt-10)
REVERT: A  630 ASP cc_start: 0.8021 (m-30) cc_final: 0.7673 (m-30)
REVERT: A  643 TRP cc_start: 0.7627 (t60) cc_final: 0.7102 (t60)
REVERT: A  644 LEU cc_start: 0.7244 (mt) cc_final: 0.6965 (mm)
REVERT: A  645 LYS cc_start: 0.7303 (tttm) cc_final: 0.7070 (tttm)
REVERT: A  810 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5812 (mpp)
REVERT: A  859 ASP cc_start: 0.7646 (m-30) cc_final: 0.7366 (t0)
REVERT: A  863 ILE cc_start: 0.6308 (mm) cc_final: 0.5996 (mm)
REVERT: A  872 GLU cc_start: 0.6814 (mm-30) cc_final: 0.5951 (mm-30)
REVERT: A  880 LYS cc_start: 0.7444 (tttt) cc_final: 0.7042 (ttpt)
REVERT: A  911 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6753 (mm-30)
REVERT: A  915 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6952 (mt-10)
REVERT: A  926 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6736 (tt0)
REVERT: A  938 MET cc_start: 0.7851 (tpp) cc_final: 0.7471 (ttt)
REVERT: A  946 SER cc_start: 0.8031 (p) cc_final: 0.7367 (t)
REVERT: A  966 ASP cc_start: 0.7317 (t0) cc_final: 0.6939 (t0)
REVERT: A  968 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7581 (mtmt)
REVERT: A  986 GLU cc_start: 0.6169 (tt0) cc_final: 0.5471 (tt0)
REVERT: A  991 GLU cc_start: 0.8087 (tt0) cc_final: 0.7483 (tp30)
REVERT: A  994 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7161 (tm-30)
REVERT: A  998 LEU cc_start: 0.6605 (mp) cc_final: 0.6373 (mt)
REVERT: A 1035 TYR cc_start: 0.7889 (m-80) cc_final: 0.7599 (m-80)
REVERT: A 1059 CYS cc_start: 0.7181 (m) cc_final: 0.6588 (m)
REVERT: A 1060 GLU cc_start: 0.7920 (tp30) cc_final: 0.7664 (tp30)
REVERT: A 1071 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7951 (tm-30)
REVERT: A 1085 SER cc_start: 0.8247 (t) cc_final: 0.7818 (p)
REVERT: A 1105 GLU cc_start: 0.8223 (tt0) cc_final: 0.7435 (pp20)
REVERT: A 1122 GLU cc_start: 0.7746 (tp30) cc_final: 0.7500 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6732 (mmm-85)
  outliers start: 27
  outliers final: 20
  residues processed: 251
  average time/residue: 0.2322
  time to fit residues: 76.1353
Evaluate side-chains
  257 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 236
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1189 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8267  Z= 0.224
  Angle     :  0.518   8.924  11218  Z= 0.265
  Chirality :  0.039   0.169   1348
  Planarity :  0.004   0.040   1378
  Dihedral  :  8.227 145.856   1104
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.05 %
    Favored  : 79.66 %
  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:  2.09 (0.27), residues: 1012
  helix:  1.99 (0.20), residues: 705
  sheet: -0.27 (0.69), residues: 61
  loop :  0.19 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 962 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.017   0.001   PHE A 739 
 TYR   0.015   0.001   TYR A 984 
 ARG   0.006   0.001   ARG A 976 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 244
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.6603 (mmt) cc_final: 0.5837 (mmt)
REVERT: A  134 ASP cc_start: 0.7630 (m-30) cc_final: 0.6573 (p0)
REVERT: A  149 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: A  154 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6797 (mtm)
REVERT: A  157 HIS cc_start: 0.7014 (m90) cc_final: 0.6437 (m-70)
REVERT: A  158 THR cc_start: 0.7119 (p) cc_final: 0.6550 (m)
REVERT: A  160 MET cc_start: 0.7374 (mmt) cc_final: 0.6873 (mmt)
REVERT: A  164 SER cc_start: 0.7493 (m) cc_final: 0.7160 (p)
REVERT: A  168 ILE cc_start: 0.6685 (tt) cc_final: 0.6322 (pt)
REVERT: A  199 MET cc_start: 0.7543 (mmm) cc_final: 0.7117 (mmm)
REVERT: A  209 ASP cc_start: 0.7316 (t0) cc_final: 0.6757 (t70)
REVERT: A  238 ASP cc_start: 0.6119 (m-30) cc_final: 0.5793 (m-30)
REVERT: A  373 THR cc_start: 0.6832 (m) cc_final: 0.6529 (m)
REVERT: A  383 MET cc_start: 0.7393 (mmm) cc_final: 0.7156 (tpp)
REVERT: A  443 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6919 (tm-30)
REVERT: A  475 GLN cc_start: 0.7385 (tp40) cc_final: 0.6848 (tp-100)
REVERT: A  485 ASP cc_start: 0.7794 (m-30) cc_final: 0.7377 (p0)
REVERT: A  486 ILE cc_start: 0.7693 (mt) cc_final: 0.7418 (tp)
REVERT: A  490 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7600 (mtmt)
REVERT: A  500 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7208 (tpp80)
REVERT: A  511 MET cc_start: 0.7872 (tmm) cc_final: 0.7632 (tmm)
REVERT: A  579 MET cc_start: 0.7091 (tmm) cc_final: 0.6742 (tmm)
REVERT: A  580 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7726 (mm-30)
REVERT: A  585 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.6978 (tpp80)
REVERT: A  588 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7190 (ttpp)
REVERT: A  599 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7212 (mt-10)
REVERT: A  616 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7449 (mm-30)
REVERT: A  643 TRP cc_start: 0.7632 (t60) cc_final: 0.7072 (t60)
REVERT: A  644 LEU cc_start: 0.7254 (mt) cc_final: 0.6994 (mm)
REVERT: A  645 LYS cc_start: 0.7263 (tttm) cc_final: 0.6944 (tttm)
REVERT: A  810 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5913 (mpp)
REVERT: A  815 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7160 (ttpp)
REVERT: A  863 ILE cc_start: 0.6260 (mm) cc_final: 0.6055 (mm)
REVERT: A  872 GLU cc_start: 0.6784 (mm-30) cc_final: 0.5877 (mm-30)
REVERT: A  880 LYS cc_start: 0.7361 (tttt) cc_final: 0.6986 (ttpt)
REVERT: A  887 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7331 (mtp85)
REVERT: A  900 GLN cc_start: 0.7414 (mt0) cc_final: 0.7133 (mm-40)
REVERT: A  911 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6771 (mm-30)
REVERT: A  915 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6947 (mt-10)
REVERT: A  926 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6730 (tt0)
REVERT: A  938 MET cc_start: 0.7838 (tpp) cc_final: 0.7450 (ttm)
REVERT: A  946 SER cc_start: 0.7978 (p) cc_final: 0.7313 (t)
REVERT: A  966 ASP cc_start: 0.7249 (t0) cc_final: 0.6925 (t0)
REVERT: A  968 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7599 (mtmt)
REVERT: A  986 GLU cc_start: 0.6312 (tt0) cc_final: 0.5620 (tt0)
REVERT: A  991 GLU cc_start: 0.8047 (tt0) cc_final: 0.7547 (tp30)
REVERT: A  994 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: A  998 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6329 (mt)
REVERT: A 1033 GLU cc_start: 0.6365 (mm-30) cc_final: 0.5959 (tp30)
REVERT: A 1035 TYR cc_start: 0.7910 (m-80) cc_final: 0.7645 (m-80)
REVERT: A 1059 CYS cc_start: 0.7185 (m) cc_final: 0.6543 (m)
REVERT: A 1060 GLU cc_start: 0.7863 (tp30) cc_final: 0.7627 (tp30)
REVERT: A 1071 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7997 (mp0)
REVERT: A 1085 SER cc_start: 0.8222 (t) cc_final: 0.7816 (p)
REVERT: A 1105 GLU cc_start: 0.8192 (tt0) cc_final: 0.7436 (pp20)
REVERT: A 1118 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7218 (mtmm)
REVERT: A 1122 GLU cc_start: 0.7748 (tp30) cc_final: 0.7491 (mm-30)
REVERT: A 1183 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7095 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7351 (mmt180) cc_final: 0.6763 (mmm-85)
  outliers start: 29
  outliers final: 19
  residues processed: 256
  average time/residue: 0.2335
  time to fit residues: 77.9767
Evaluate side-chains
  264 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1129 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0070
   chunk 24 optimal weight:    0.0670
   chunk 33 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.3014

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8267  Z= 0.160
  Angle     :  0.507   8.965  11218  Z= 0.256
  Chirality :  0.038   0.193   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.173 146.038   1104
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.61 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.27), residues: 1012
  helix:  2.13 (0.20), residues: 707
  sheet: -0.05 (0.71), residues: 59
  loop :  0.09 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 157 
 PHE   0.018   0.001   PHE A 972 
 TYR   0.013   0.001   TYR A 984 
 ARG   0.005   0.000   ARG A 583 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.6952 (mm) cc_final: 0.6648 (mt)
REVERT: A  134 ASP cc_start: 0.7618 (m-30) cc_final: 0.6970 (t0)
REVERT: A  149 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6590 (tm-30)
REVERT: A  155 ASP cc_start: 0.6223 (p0) cc_final: 0.5879 (p0)
REVERT: A  157 HIS cc_start: 0.6658 (m90) cc_final: 0.5297 (m90)
REVERT: A  160 MET cc_start: 0.7406 (mmt) cc_final: 0.6871 (mmt)
REVERT: A  161 ARG cc_start: 0.7735 (tpp80) cc_final: 0.7018 (mpp80)
REVERT: A  164 SER cc_start: 0.7479 (m) cc_final: 0.7233 (p)
REVERT: A  209 ASP cc_start: 0.7325 (t0) cc_final: 0.6721 (t70)
REVERT: A  238 ASP cc_start: 0.6148 (m-30) cc_final: 0.5799 (m-30)
REVERT: A  383 MET cc_start: 0.7366 (mmm) cc_final: 0.7138 (tpp)
REVERT: A  443 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7051 (tp30)
REVERT: A  475 GLN cc_start: 0.7369 (tp40) cc_final: 0.6858 (tp-100)
REVERT: A  485 ASP cc_start: 0.7902 (m-30) cc_final: 0.7438 (p0)
REVERT: A  486 ILE cc_start: 0.7659 (mt) cc_final: 0.7435 (tp)
REVERT: A  500 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7197 (tpp80)
REVERT: A  511 MET cc_start: 0.7893 (tmm) cc_final: 0.7651 (tmm)
REVERT: A  583 ARG cc_start: 0.7687 (ttt-90) cc_final: 0.7469 (ttt-90)
REVERT: A  585 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6941 (tpp80)
REVERT: A  588 LYS cc_start: 0.7598 (ttpp) cc_final: 0.7168 (ttpp)
REVERT: A  599 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7222 (mt-10)
REVERT: A  643 TRP cc_start: 0.7621 (t60) cc_final: 0.7090 (t60)
REVERT: A  644 LEU cc_start: 0.7220 (mt) cc_final: 0.6991 (mm)
REVERT: A  810 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5860 (mpp)
REVERT: A  815 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7159 (ttpp)
REVERT: A  857 MET cc_start: 0.7330 (tpp) cc_final: 0.6943 (tpp)
REVERT: A  863 ILE cc_start: 0.6198 (mm) cc_final: 0.5939 (mm)
REVERT: A  872 GLU cc_start: 0.6675 (mm-30) cc_final: 0.5919 (mm-30)
REVERT: A  880 LYS cc_start: 0.7435 (tttt) cc_final: 0.7018 (ttpt)
REVERT: A  887 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7293 (mtp85)
REVERT: A  900 GLN cc_start: 0.7324 (mt0) cc_final: 0.7098 (mm-40)
REVERT: A  911 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6765 (mm-30)
REVERT: A  915 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6942 (mt-10)
REVERT: A  926 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6699 (tt0)
REVERT: A  938 MET cc_start: 0.7947 (tpp) cc_final: 0.7583 (ttm)
REVERT: A  946 SER cc_start: 0.7977 (p) cc_final: 0.7247 (t)
REVERT: A  966 ASP cc_start: 0.7265 (t0) cc_final: 0.6919 (t0)
REVERT: A  968 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7594 (mtmt)
REVERT: A  991 GLU cc_start: 0.8041 (tt0) cc_final: 0.7463 (tp30)
REVERT: A  994 GLU cc_start: 0.7299 (tm-30) cc_final: 0.7097 (tm-30)
REVERT: A  998 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6354 (mt)
REVERT: A 1033 GLU cc_start: 0.6447 (mm-30) cc_final: 0.5966 (tp30)
REVERT: A 1035 TYR cc_start: 0.7905 (m-80) cc_final: 0.7486 (m-80)
REVERT: A 1059 CYS cc_start: 0.7177 (m) cc_final: 0.6523 (m)
REVERT: A 1060 GLU cc_start: 0.7843 (tp30) cc_final: 0.7590 (tp30)
REVERT: A 1071 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7955 (mp0)
REVERT: A 1082 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6194 (tt)
REVERT: A 1085 SER cc_start: 0.8245 (t) cc_final: 0.7813 (p)
REVERT: A 1105 GLU cc_start: 0.8171 (tt0) cc_final: 0.7417 (pp20)
REVERT: A 1183 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6638 (tp30)
REVERT: A 1190 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6739 (mmm-85)
  outliers start: 26
  outliers final: 14
  residues processed: 244
  average time/residue: 0.2380
  time to fit residues: 75.9898
Evaluate side-chains
  253 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 235
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1113 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 24 optimal weight:    0.3980
   chunk 98 optimal weight:    0.0980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 95 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8267  Z= 0.177
  Angle     :  0.511   8.965  11218  Z= 0.255
  Chirality :  0.038   0.202   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.139 145.920   1104
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.64 %
    Favored  : 78.41 %
  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:  2.20 (0.27), residues: 1012
  helix:  2.10 (0.20), residues: 706
  sheet: -0.09 (0.69), residues: 61
  loop :  0.03 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 962 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 625 
 TYR   0.009   0.001   TYR A 984 
 ARG   0.007   0.000   ARG A 812 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 238
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6358 (mppt) cc_final: 0.5984 (mppt)
REVERT: A  108 ILE cc_start: 0.6949 (mm) cc_final: 0.6642 (mt)
REVERT: A  134 ASP cc_start: 0.7619 (m-30) cc_final: 0.6957 (t0)
REVERT: A  149 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6588 (tm-30)
REVERT: A  155 ASP cc_start: 0.6463 (p0) cc_final: 0.6071 (p0)
REVERT: A  157 HIS cc_start: 0.6740 (m90) cc_final: 0.5416 (m90)
REVERT: A  160 MET cc_start: 0.7384 (mmt) cc_final: 0.6856 (mmt)
REVERT: A  161 ARG cc_start: 0.7720 (tpp80) cc_final: 0.6949 (mpp80)
REVERT: A  168 ILE cc_start: 0.6642 (tt) cc_final: 0.6317 (pt)
REVERT: A  238 ASP cc_start: 0.6177 (m-30) cc_final: 0.5831 (m-30)
REVERT: A  383 MET cc_start: 0.7362 (mmm) cc_final: 0.7152 (tpp)
REVERT: A  443 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  475 GLN cc_start: 0.7356 (tp40) cc_final: 0.6851 (tp-100)
REVERT: A  485 ASP cc_start: 0.7896 (m-30) cc_final: 0.7439 (p0)
REVERT: A  486 ILE cc_start: 0.7664 (mt) cc_final: 0.7438 (tp)
REVERT: A  500 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7211 (tpp80)
REVERT: A  511 MET cc_start: 0.7874 (tmm) cc_final: 0.7614 (tmm)
REVERT: A  579 MET cc_start: 0.7114 (tmm) cc_final: 0.6504 (tmm)
REVERT: A  580 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7543 (mm-30)
REVERT: A  588 LYS cc_start: 0.7589 (ttpp) cc_final: 0.7202 (ttpp)
REVERT: A  599 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7173 (mt-10)
REVERT: A  643 TRP cc_start: 0.7624 (t60) cc_final: 0.7092 (t60)
REVERT: A  810 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5766 (mpp)
REVERT: A  872 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6442 (mm-30)
REVERT: A  880 LYS cc_start: 0.7448 (tttt) cc_final: 0.7032 (ttpt)
REVERT: A  887 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7270 (mtp85)
REVERT: A  900 GLN cc_start: 0.7325 (mt0) cc_final: 0.7083 (mm-40)
REVERT: A  911 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6769 (mm-30)
REVERT: A  915 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6939 (mt-10)
REVERT: A  926 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6746 (tt0)
REVERT: A  938 MET cc_start: 0.7917 (tpp) cc_final: 0.7586 (ttm)
REVERT: A  946 SER cc_start: 0.8040 (p) cc_final: 0.7267 (t)
REVERT: A  966 ASP cc_start: 0.7278 (t0) cc_final: 0.6982 (t0)
REVERT: A  991 GLU cc_start: 0.8053 (tt0) cc_final: 0.7521 (tp30)
REVERT: A  994 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7047 (tm-30)
REVERT: A 1033 GLU cc_start: 0.6495 (mm-30) cc_final: 0.5978 (tp30)
REVERT: A 1035 TYR cc_start: 0.7909 (m-80) cc_final: 0.7539 (m-80)
REVERT: A 1059 CYS cc_start: 0.7153 (m) cc_final: 0.6527 (m)
REVERT: A 1060 GLU cc_start: 0.7848 (tp30) cc_final: 0.7543 (tp30)
REVERT: A 1071 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7918 (mp0)
REVERT: A 1082 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6262 (tt)
REVERT: A 1085 SER cc_start: 0.8271 (t) cc_final: 0.7850 (p)
REVERT: A 1110 GLN cc_start: 0.7840 (mp10) cc_final: 0.7618 (mp10)
REVERT: A 1122 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7262 (mm-30)
REVERT: A 1183 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6633 (tp30)
REVERT: A 1190 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6774 (mmm-85)
  outliers start: 26
  outliers final: 16
  residues processed: 248
  average time/residue: 0.2251
  time to fit residues: 73.4502
Evaluate side-chains
  252 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 234
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1113 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.0970
   chunk 55 optimal weight:    0.0870
   chunk 83 optimal weight:    0.4980
   chunk 98 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6678
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8267  Z= 0.165
  Angle     :  0.508   8.927  11218  Z= 0.254
  Chirality :  0.038   0.209   1348
  Planarity :  0.004   0.043   1378
  Dihedral  :  8.141 146.473   1104
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 19.77 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 1012
  helix:  2.21 (0.20), residues: 702
  sheet: -0.05 (0.69), residues: 61
  loop : -0.01 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A1120 
 PHE   0.017   0.001   PHE A 625 
 TYR   0.006   0.001   TYR A 743 
 ARG   0.006   0.000   ARG A 812 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 231
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6375 (mppt) cc_final: 0.5995 (mppt)
REVERT: A  108 ILE cc_start: 0.6933 (mm) cc_final: 0.6624 (mt)
REVERT: A  134 ASP cc_start: 0.7608 (m-30) cc_final: 0.6963 (t0)
REVERT: A  149 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6584 (tm-30)
REVERT: A  155 ASP cc_start: 0.6551 (p0) cc_final: 0.6148 (p0)
REVERT: A  157 HIS cc_start: 0.6717 (m90) cc_final: 0.6307 (m90)
REVERT: A  160 MET cc_start: 0.7438 (mmt) cc_final: 0.7164 (mmt)
REVERT: A  199 MET cc_start: 0.7499 (mmm) cc_final: 0.6776 (tpp)
REVERT: A  238 ASP cc_start: 0.6218 (m-30) cc_final: 0.5824 (m-30)
REVERT: A  443 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6938 (tm-30)
REVERT: A  475 GLN cc_start: 0.7375 (tp40) cc_final: 0.6982 (tp40)
REVERT: A  485 ASP cc_start: 0.7918 (m-30) cc_final: 0.7380 (p0)
REVERT: A  486 ILE cc_start: 0.7653 (mt) cc_final: 0.7304 (tp)
REVERT: A  500 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7197 (tpp80)
REVERT: A  511 MET cc_start: 0.7864 (tmm) cc_final: 0.7618 (tmm)
REVERT: A  579 MET cc_start: 0.7027 (tmm) cc_final: 0.6745 (tmm)
REVERT: A  580 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7715 (mm-30)
REVERT: A  585 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6779 (ttp-170)
REVERT: A  586 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6921 (ttp)
REVERT: A  588 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7186 (ttpp)
REVERT: A  599 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7120 (mt-10)
REVERT: A  643 TRP cc_start: 0.7712 (t60) cc_final: 0.7289 (t60)
REVERT: A  810 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5740 (mpp)
REVERT: A  849 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7082 (mm-30)
REVERT: A  880 LYS cc_start: 0.7438 (tttt) cc_final: 0.7016 (ttpt)
REVERT: A  887 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7357 (mtp85)
REVERT: A  900 GLN cc_start: 0.7319 (mt0) cc_final: 0.7073 (mm-40)
REVERT: A  911 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6806 (mm-30)
REVERT: A  915 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6957 (mt-10)
REVERT: A  926 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6706 (tt0)
REVERT: A  938 MET cc_start: 0.7935 (tpp) cc_final: 0.7611 (ttm)
REVERT: A  946 SER cc_start: 0.8061 (p) cc_final: 0.7278 (t)
REVERT: A  966 ASP cc_start: 0.7263 (t0) cc_final: 0.6936 (t0)
REVERT: A  986 GLU cc_start: 0.6429 (tt0) cc_final: 0.5274 (tt0)
REVERT: A  991 GLU cc_start: 0.8038 (tt0) cc_final: 0.7539 (tp30)
REVERT: A  994 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7056 (tm-30)
REVERT: A 1033 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6108 (tp30)
REVERT: A 1035 TYR cc_start: 0.7903 (m-80) cc_final: 0.7557 (m-80)
REVERT: A 1050 LYS cc_start: 0.7420 (mmmt) cc_final: 0.7218 (mmmt)
REVERT: A 1059 CYS cc_start: 0.7093 (m) cc_final: 0.6413 (m)
REVERT: A 1060 GLU cc_start: 0.7808 (tp30) cc_final: 0.7504 (tp30)
REVERT: A 1071 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7873 (mp0)
REVERT: A 1082 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6294 (tt)
REVERT: A 1085 SER cc_start: 0.8298 (t) cc_final: 0.7891 (p)
REVERT: A 1183 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6638 (tp30)
REVERT: A 1190 ARG cc_start: 0.7387 (mmt180) cc_final: 0.6763 (mmm-85)
  outliers start: 22
  outliers final: 15
  residues processed: 240
  average time/residue: 0.2307
  time to fit residues: 72.8144
Evaluate side-chains
  246 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 228
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1082 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0570
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8267  Z= 0.206
  Angle     :  0.523   8.936  11218  Z= 0.261
  Chirality :  0.039   0.211   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.154 146.114   1104
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.34 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.27), residues: 1012
  helix:  2.11 (0.20), residues: 702
  sheet: -0.19 (0.68), residues: 61
  loop : -0.10 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 962 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 625 
 TYR   0.008   0.001   TYR A1088 
 ARG   0.006   0.001   ARG A 812 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 231
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6379 (mppt) cc_final: 0.6004 (mppt)
REVERT: A  108 ILE cc_start: 0.6939 (mm) cc_final: 0.6636 (mt)
REVERT: A  134 ASP cc_start: 0.7605 (m-30) cc_final: 0.6970 (t0)
REVERT: A  149 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: A  155 ASP cc_start: 0.6661 (p0) cc_final: 0.6203 (p0)
REVERT: A  157 HIS cc_start: 0.6890 (m90) cc_final: 0.6524 (m90)
REVERT: A  160 MET cc_start: 0.7447 (mmt) cc_final: 0.7199 (mmt)
REVERT: A  199 MET cc_start: 0.7448 (mmm) cc_final: 0.6713 (tpp)
REVERT: A  209 ASP cc_start: 0.7264 (t0) cc_final: 0.6857 (t0)
REVERT: A  238 ASP cc_start: 0.6244 (m-30) cc_final: 0.5865 (m-30)
REVERT: A  401 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6517 (tmm)
REVERT: A  443 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6913 (tm-30)
REVERT: A  475 GLN cc_start: 0.7363 (tp40) cc_final: 0.6985 (tp40)
REVERT: A  485 ASP cc_start: 0.7914 (m-30) cc_final: 0.7378 (p0)
REVERT: A  486 ILE cc_start: 0.7668 (mt) cc_final: 0.7315 (tp)
REVERT: A  500 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7190 (tpp80)
REVERT: A  511 MET cc_start: 0.7884 (tmm) cc_final: 0.7628 (tmm)
REVERT: A  573 ARG cc_start: 0.6848 (tpp80) cc_final: 0.6521 (tpp80)
REVERT: A  579 MET cc_start: 0.7034 (tmm) cc_final: 0.6749 (tmm)
REVERT: A  580 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7821 (mm-30)
REVERT: A  585 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6724 (ttp-170)
REVERT: A  586 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6945 (ttp)
REVERT: A  588 LYS cc_start: 0.7590 (ttpp) cc_final: 0.7205 (ttpp)
REVERT: A  599 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7195 (mt-10)
REVERT: A  643 TRP cc_start: 0.7700 (t60) cc_final: 0.7276 (t60)
REVERT: A  810 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.5700 (mpp)
REVERT: A  849 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7025 (mm-30)
REVERT: A  863 ILE cc_start: 0.6206 (mm) cc_final: 0.5897 (mt)
REVERT: A  872 GLU cc_start: 0.6697 (mm-30) cc_final: 0.5952 (mm-30)
REVERT: A  880 LYS cc_start: 0.7438 (tttt) cc_final: 0.6995 (ttpt)
REVERT: A  887 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7348 (mtp85)
REVERT: A  900 GLN cc_start: 0.7325 (mt0) cc_final: 0.7091 (mm-40)
REVERT: A  911 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6815 (mm-30)
REVERT: A  915 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6945 (mt-10)
REVERT: A  926 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6717 (tt0)
REVERT: A  938 MET cc_start: 0.7933 (tpp) cc_final: 0.7612 (ttm)
REVERT: A  946 SER cc_start: 0.8065 (p) cc_final: 0.7279 (t)
REVERT: A  966 ASP cc_start: 0.7287 (t0) cc_final: 0.6655 (p0)
REVERT: A  986 GLU cc_start: 0.6491 (tt0) cc_final: 0.5457 (tt0)
REVERT: A  991 GLU cc_start: 0.8037 (tt0) cc_final: 0.7560 (tp30)
REVERT: A 1009 TYR cc_start: 0.6881 (t80) cc_final: 0.6662 (t80)
REVERT: A 1033 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6114 (tp30)
REVERT: A 1035 TYR cc_start: 0.7884 (m-80) cc_final: 0.7530 (m-80)
REVERT: A 1050 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7313 (mmmt)
REVERT: A 1059 CYS cc_start: 0.7189 (m) cc_final: 0.6521 (m)
REVERT: A 1060 GLU cc_start: 0.7844 (tp30) cc_final: 0.7534 (tp30)
REVERT: A 1071 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7862 (mp0)
REVERT: A 1082 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6334 (tt)
REVERT: A 1085 SER cc_start: 0.8325 (t) cc_final: 0.7927 (p)
REVERT: A 1183 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6636 (tp30)
REVERT: A 1190 ARG cc_start: 0.7353 (mmt180) cc_final: 0.6754 (mmm-85)
  outliers start: 23
  outliers final: 12
  residues processed: 241
  average time/residue: 0.2280
  time to fit residues: 72.2770
Evaluate side-chains
  244 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1113 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0570
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8267  Z= 0.209
  Angle     :  0.537   9.754  11218  Z= 0.270
  Chirality :  0.039   0.216   1348
  Planarity :  0.004   0.042   1378
  Dihedral  :  8.173 146.230   1104
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.91 %
    Favored  : 76.36 %
  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:  2.12 (0.27), residues: 1012
  helix:  2.11 (0.20), residues: 702
  sheet: -0.14 (0.69), residues: 61
  loop : -0.17 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 635 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 625 
 TYR   0.008   0.001   TYR A1088 
 ARG   0.007   0.000   ARG A 812 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 230
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6375 (mppt) cc_final: 0.5992 (mppt)
REVERT: A  108 ILE cc_start: 0.6939 (mm) cc_final: 0.6634 (mt)
REVERT: A  134 ASP cc_start: 0.7605 (m-30) cc_final: 0.6971 (t0)
REVERT: A  149 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6590 (tm-30)
REVERT: A  155 ASP cc_start: 0.6680 (p0) cc_final: 0.6291 (p0)
REVERT: A  157 HIS cc_start: 0.6880 (m90) cc_final: 0.6499 (m90)
REVERT: A  160 MET cc_start: 0.7503 (mmt) cc_final: 0.7260 (mmt)
REVERT: A  168 ILE cc_start: 0.6665 (tt) cc_final: 0.6338 (pt)
REVERT: A  199 MET cc_start: 0.7362 (mmm) cc_final: 0.6664 (tpp)
REVERT: A  209 ASP cc_start: 0.7330 (t0) cc_final: 0.6928 (t0)
REVERT: A  238 ASP cc_start: 0.6256 (m-30) cc_final: 0.5886 (m-30)
REVERT: A  401 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6535 (tmm)
REVERT: A  443 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  475 GLN cc_start: 0.7357 (tp40) cc_final: 0.6981 (tp40)
REVERT: A  485 ASP cc_start: 0.7918 (m-30) cc_final: 0.7374 (p0)
REVERT: A  486 ILE cc_start: 0.7673 (mt) cc_final: 0.7325 (tp)
REVERT: A  500 ARG cc_start: 0.7510 (tpp80) cc_final: 0.7301 (ttm110)
REVERT: A  511 MET cc_start: 0.7885 (tmm) cc_final: 0.7627 (tmm)
REVERT: A  573 ARG cc_start: 0.6880 (tpp80) cc_final: 0.6560 (tpp80)
REVERT: A  579 MET cc_start: 0.7032 (tmm) cc_final: 0.6720 (tmm)
REVERT: A  586 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6932 (ttp)
REVERT: A  588 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7205 (ttpp)
REVERT: A  599 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7139 (mt-10)
REVERT: A  628 VAL cc_start: 0.7637 (m) cc_final: 0.6943 (m)
REVERT: A  643 TRP cc_start: 0.7705 (t60) cc_final: 0.7297 (t60)
REVERT: A  810 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5726 (mpp)
REVERT: A  863 ILE cc_start: 0.6251 (mm) cc_final: 0.5869 (mt)
REVERT: A  872 GLU cc_start: 0.6685 (mm-30) cc_final: 0.5957 (mm-30)
REVERT: A  880 LYS cc_start: 0.7378 (tttt) cc_final: 0.6938 (ttpt)
REVERT: A  887 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.7358 (mtp85)
REVERT: A  900 GLN cc_start: 0.7336 (mt0) cc_final: 0.7094 (mm-40)
REVERT: A  911 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6814 (mm-30)
REVERT: A  915 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6953 (mt-10)
REVERT: A  926 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6718 (tt0)
REVERT: A  938 MET cc_start: 0.7936 (tpp) cc_final: 0.7613 (ttm)
REVERT: A  946 SER cc_start: 0.8014 (p) cc_final: 0.7263 (t)
REVERT: A  966 ASP cc_start: 0.7281 (t0) cc_final: 0.6637 (p0)
REVERT: A  986 GLU cc_start: 0.6485 (tt0) cc_final: 0.5448 (tt0)
REVERT: A  991 GLU cc_start: 0.8038 (tt0) cc_final: 0.7544 (tp30)
REVERT: A 1033 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6115 (tp30)
REVERT: A 1035 TYR cc_start: 0.7893 (m-80) cc_final: 0.7534 (m-80)
REVERT: A 1050 LYS cc_start: 0.7565 (mmmt) cc_final: 0.7339 (mmmt)
REVERT: A 1059 CYS cc_start: 0.7211 (m) cc_final: 0.6537 (m)
REVERT: A 1060 GLU cc_start: 0.7855 (tp30) cc_final: 0.7528 (tp30)
REVERT: A 1082 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6353 (tt)
REVERT: A 1085 SER cc_start: 0.8330 (t) cc_final: 0.7938 (p)
REVERT: A 1183 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6637 (tp30)
REVERT: A 1190 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6745 (mmm-85)
  outliers start: 24
  outliers final: 16
  residues processed: 240
  average time/residue: 0.2405
  time to fit residues: 75.2028
Evaluate side-chains
  245 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 225
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  729 GLU
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1082 LEU
Chi-restraints excluded: chain A residue 1113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0870
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 49 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0570
   chunk 74 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8267  Z= 0.181
  Angle     :  0.546   9.748  11218  Z= 0.274
  Chirality :  0.039   0.172   1348
  Planarity :  0.004   0.047   1378
  Dihedral  :  8.178 146.550   1104
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.70 %
    Favored  : 76.14 %
  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:  2.10 (0.27), residues: 1012
  helix:  2.08 (0.20), residues: 704
  sheet: -0.16 (0.70), residues: 61
  loop : -0.13 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A1120 
 PHE   0.017   0.001   PHE A 625 
 TYR   0.017   0.001   TYR A 267 
 ARG   0.006   0.001   ARG A 812 

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 230
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6374 (mppt) cc_final: 0.5990 (mppt)
REVERT: A  108 ILE cc_start: 0.6932 (mm) cc_final: 0.6618 (mt)
REVERT: A  134 ASP cc_start: 0.7599 (m-30) cc_final: 0.6973 (t0)
REVERT: A  149 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6595 (tm-30)
REVERT: A  155 ASP cc_start: 0.6685 (p0) cc_final: 0.6255 (p0)
REVERT: A  157 HIS cc_start: 0.6889 (m90) cc_final: 0.6511 (m90)
REVERT: A  160 MET cc_start: 0.7495 (mmt) cc_final: 0.7259 (mmt)
REVERT: A  199 MET cc_start: 0.7480 (mmm) cc_final: 0.6765 (tpp)
REVERT: A  209 ASP cc_start: 0.7281 (t0) cc_final: 0.6906 (t0)
REVERT: A  238 ASP cc_start: 0.6240 (m-30) cc_final: 0.5848 (m-30)
REVERT: A  401 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6546 (tmm)
REVERT: A  475 GLN cc_start: 0.7357 (tp40) cc_final: 0.6978 (tp40)
REVERT: A  485 ASP cc_start: 0.7914 (m-30) cc_final: 0.7358 (p0)
REVERT: A  486 ILE cc_start: 0.7665 (mt) cc_final: 0.7320 (tp)
REVERT: A  500 ARG cc_start: 0.7508 (tpp80) cc_final: 0.7189 (tpp80)
REVERT: A  511 MET cc_start: 0.7882 (tmm) cc_final: 0.7632 (tmm)
REVERT: A  573 ARG cc_start: 0.6858 (tpp80) cc_final: 0.6548 (tpp80)
REVERT: A  579 MET cc_start: 0.6782 (tmm) cc_final: 0.6576 (tmm)
REVERT: A  586 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6898 (ttp)
REVERT: A  588 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7205 (ttpp)
REVERT: A  595 TRP cc_start: 0.7475 (m100) cc_final: 0.7259 (m100)
REVERT: A  599 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7372 (mt-10)
REVERT: A  616 GLU cc_start: 0.6815 (pp20) cc_final: 0.6451 (pp20)
REVERT: A  628 VAL cc_start: 0.7610 (m) cc_final: 0.7280 (p)
REVERT: A  633 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8101 (mtmm)
REVERT: A  643 TRP cc_start: 0.7695 (t60) cc_final: 0.7275 (t60)
REVERT: A  810 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5677 (mpp)
REVERT: A  863 ILE cc_start: 0.6313 (mm) cc_final: 0.6016 (mt)
REVERT: A  880 LYS cc_start: 0.7314 (tttt) cc_final: 0.6864 (ttpt)
REVERT: A  887 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7307 (mtp85)
REVERT: A  900 GLN cc_start: 0.7314 (mt0) cc_final: 0.7078 (mm-40)
REVERT: A  911 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6808 (mm-30)
REVERT: A  915 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6949 (mt-10)
REVERT: A  926 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6760 (tt0)
REVERT: A  938 MET cc_start: 0.7919 (tpp) cc_final: 0.7613 (ttm)
REVERT: A  946 SER cc_start: 0.7982 (p) cc_final: 0.7197 (t)
REVERT: A  966 ASP cc_start: 0.7283 (t0) cc_final: 0.6639 (p0)
REVERT: A  986 GLU cc_start: 0.6475 (tt0) cc_final: 0.5460 (tt0)
REVERT: A  991 GLU cc_start: 0.8065 (tt0) cc_final: 0.7562 (tp30)
REVERT: A 1009 TYR cc_start: 0.6889 (t80) cc_final: 0.6688 (t80)
REVERT: A 1033 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6279 (tp30)
REVERT: A 1035 TYR cc_start: 0.7903 (m-80) cc_final: 0.7510 (m-80)
REVERT: A 1050 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7381 (mmmt)
REVERT: A 1059 CYS cc_start: 0.7163 (m) cc_final: 0.6497 (m)
REVERT: A 1060 GLU cc_start: 0.7848 (tp30) cc_final: 0.7530 (tp30)
REVERT: A 1081 THR cc_start: 0.8304 (p) cc_final: 0.8080 (m)
REVERT: A 1082 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6303 (tt)
REVERT: A 1085 SER cc_start: 0.8324 (t) cc_final: 0.7936 (p)
REVERT: A 1122 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: A 1183 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6819 (tp30)
REVERT: A 1190 ARG cc_start: 0.7323 (mmt180) cc_final: 0.6745 (mmm-85)
  outliers start: 19
  outliers final: 12
  residues processed: 237
  average time/residue: 0.2336
  time to fit residues: 72.6552
Evaluate side-chains
  245 residues out of total 880 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 229
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  810 MET
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1082 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.0170
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0970
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111761 restraints weight = 12818.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114977 restraints weight = 5978.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.117011 restraints weight = 3500.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8267  Z= 0.193
  Angle     :  0.551   9.051  11218  Z= 0.281
  Chirality :  0.039   0.183   1348
  Planarity :  0.004   0.043   1378
  Dihedral  :  8.179 146.523   1104
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.05 %
    Favored  : 75.68 %
  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:  2.06 (0.27), residues: 1012
  helix:  2.04 (0.20), residues: 704
  sheet: -0.12 (0.71), residues: 61
  loop : -0.14 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.031   0.001   PHE A 268 
 TYR   0.016   0.001   TYR A 267 
 ARG   0.006   0.000   ARG A 812 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2244.14 seconds
wall clock time: 41 minutes 11.59 seconds (2471.59 seconds total)